From 27971d5f88fd51d842391c87b993dbe3cd69bf6b Mon Sep 17 00:00:00 2001 From: Istaisa <32853927+Istaisa@users.noreply.github.com> Date: Mon, 13 Apr 2026 13:19:49 +0100 Subject: [PATCH 1/3] Remove b37 TSO500 DNA --- 2_TSO500.sh | 273 +--- TSO_extra_padding_chr.interval_list | 714 ---------- hotspot_coverage/Colorectal_combined.bed | 38 - hotspot_coverage/Colorectal_combined.groups | 39 - hotspot_coverage/Colorectal_genescreen.bed | 20 - hotspot_coverage/Colorectal_genescreen.groups | 21 - hotspot_coverage/Colorectal_hotspots.bed | 18 - hotspot_coverage/Colorectal_hotspots.groups | 19 - hotspot_coverage/GIST_combined.bed | 8 - hotspot_coverage/GIST_combined.groups | 9 - hotspot_coverage/GIST_hotspots.bed | 8 - hotspot_coverage/GIST_hotspots.groups | 9 - hotspot_coverage/Glioma_combined.bed | 69 - hotspot_coverage/Glioma_combined.groups | 70 - hotspot_coverage/Glioma_genescreen.bed | 58 - hotspot_coverage/Glioma_genescreen.groups | 59 - hotspot_coverage/Glioma_hotspots.bed | 11 - hotspot_coverage/Glioma_hotspots.groups | 12 - hotspot_coverage/Lung_combined.bed | 11 - hotspot_coverage/Lung_combined.groups | 12 - hotspot_coverage/Lung_hotspots.bed | 11 - hotspot_coverage/Lung_hotspots.groups | 12 - hotspot_coverage/Melanoma_combined.bed | 12 - hotspot_coverage/Melanoma_combined.groups | 13 - hotspot_coverage/Melanoma_hotspots.bed | 12 - hotspot_coverage/Melanoma_hotspots.groups | 13 - hotspot_coverage/Thyroid_combined.bed | 44 - hotspot_coverage/Thyroid_combined.groups | 45 - hotspot_coverage/Thyroid_genescreen.bed | 31 - hotspot_coverage/Thyroid_genescreen.groups | 32 - hotspot_coverage/Thyroid_hotspots.bed | 13 - hotspot_coverage/Thyroid_hotspots.groups | 14 - hotspot_coverage/Tumour_combined.bed | 185 --- hotspot_coverage/Tumour_combined.groups | 186 --- hotspot_coverage/Tumour_genescreen.bed | 134 -- hotspot_coverage/Tumour_genescreen.groups | 135 -- hotspot_coverage/Tumour_hotspots.bed | 56 - hotspot_coverage/Tumour_hotspots.groups | 57 - hotspot_coverage/aitcl_combined.bed | 35 - hotspot_coverage/aitcl_combined.groups | 36 - hotspot_coverage/aitcl_genescreen.bed | 35 - hotspot_coverage/aitcl_genescreen.groups | 36 - hotspot_coverage/aitcl_hotspots.bed | 4 - hotspot_coverage/aitcl_hotspots.groups | 5 - hotspot_coverage/aml_combined.bed | 17 - hotspot_coverage/aml_combined.groups | 18 - hotspot_coverage/aml_genescreen.bed | 17 - hotspot_coverage/aml_genescreen.groups | 18 - hotspot_coverage/breast_combined.bed | 3 - hotspot_coverage/breast_combined.groups | 4 - hotspot_coverage/breast_hotspots.bed | 8 - hotspot_coverage/breast_hotspots.groups | 9 - hotspot_coverage/cll_combined.bed | 10 - hotspot_coverage/cll_combined.groups | 11 - hotspot_coverage/cll_genescreen.bed | 10 - hotspot_coverage/cll_genescreen.groups | 11 - .../endometrial-pole-tp53_combined.bed | 17 - .../endometrial-pole-tp53_combined.groups | 18 - .../endometrial-pole-tp53_genescreen.bed | 17 - .../endometrial-pole-tp53_genescreen.groups | 18 - .../endometrial-pole-tp53_hotspots.bed | 11 - .../endometrial-pole-tp53_hotspots.groups | 12 - .../endometrial-pole_combined.bed | 6 - .../endometrial-pole_combined.groups | 7 - .../endometrial-pole_genescreen.bed | 6 - .../endometrial-pole_genescreen.groups | 7 - .../endometrial-pole_hotspots.bed | 11 - .../endometrial-pole_hotspots.groups | 12 - hotspot_coverage/fight-209_combined.bed | 49 - hotspot_coverage/fight-209_combined.groups | 50 - hotspot_coverage/fight-209_hotspots.bed | 57 - hotspot_coverage/fight-209_hotspots.groups | 58 - hotspot_coverage/mpn_combined.bed | 4 - hotspot_coverage/mpn_combined.groups | 5 - hotspot_coverage/mpn_genescreen.bed | 4 - hotspot_coverage/mpn_genescreen.groups | 5 - hotspot_coverage/myeloid_combined.bed | 132 -- hotspot_coverage/myeloid_combined.groups | 133 -- hotspot_coverage/myeloid_genescreen.bed | 132 -- hotspot_coverage/myeloid_genescreen.groups | 133 -- hotspot_variants/Colorectal.bed | 34 - hotspot_variants/GIST.bed | 8 - hotspot_variants/Glioma.bed | 68 - hotspot_variants/Lung.bed | 9 - hotspot_variants/Melanoma.bed | 10 - hotspot_variants/Thyroid.bed | 40 - hotspot_variants/Tumour.bed | 194 --- hotspot_variants/aitcl.bed | 35 - hotspot_variants/aml.bed | 17 - hotspot_variants/breast.bed | 3 - hotspot_variants/cll.bed | 10 - hotspot_variants/endometrial-pole-tp53.bed | 17 - hotspot_variants/endometrial-pole.bed | 6 - hotspot_variants/fight-209.bed | 57 - hotspot_variants/mpn.bed | 4 - hotspot_variants/myeloid.bed | 130 -- preferred_transcripts.txt | 38 - rerun_coverage.sh | 267 ---- scripts/call_extra_padding_variants.sh | 203 --- scripts/coverage2json.py | 541 -------- scripts/filter_extra_padding_variants.py | 88 -- scripts/gather_list.py | 23 - scripts/keep_blacklisted_variants.py | 106 -- scripts/tsv2db.py | 163 --- tests/test_data_tsv2db/NTC_fake_variants.tsv | 43 - tests/test_data_tsv2db/NTC_no_var.tsv | 40 - tests/test_data_tsv2db/NTC_novar_blanks.tsv | 44 - .../sample_CombinedVariantOutput.tsv | 76 - .../sample_CombinedVariantOutput_blanks.tsv | 78 -- .../sample_CombinedVariantOutput_novar.tsv | 42 - tests/test_tsv2db.py | 103 -- vendorCaptureBed_100pad_updated.bed | 1230 ----------------- 112 files changed, 10 insertions(+), 7391 deletions(-) delete mode 100644 TSO_extra_padding_chr.interval_list delete mode 100644 hotspot_coverage/Colorectal_combined.bed delete mode 100644 hotspot_coverage/Colorectal_combined.groups delete mode 100644 hotspot_coverage/Colorectal_genescreen.bed delete mode 100644 hotspot_coverage/Colorectal_genescreen.groups delete mode 100644 hotspot_coverage/Colorectal_hotspots.bed delete mode 100644 hotspot_coverage/Colorectal_hotspots.groups delete mode 100644 hotspot_coverage/GIST_combined.bed delete mode 100644 hotspot_coverage/GIST_combined.groups delete mode 100644 hotspot_coverage/GIST_hotspots.bed delete mode 100644 hotspot_coverage/GIST_hotspots.groups delete mode 100644 hotspot_coverage/Glioma_combined.bed delete mode 100644 hotspot_coverage/Glioma_combined.groups delete mode 100644 hotspot_coverage/Glioma_genescreen.bed delete mode 100644 hotspot_coverage/Glioma_genescreen.groups delete mode 100644 hotspot_coverage/Glioma_hotspots.bed delete mode 100644 hotspot_coverage/Glioma_hotspots.groups delete mode 100644 hotspot_coverage/Lung_combined.bed delete mode 100644 hotspot_coverage/Lung_combined.groups delete mode 100644 hotspot_coverage/Lung_hotspots.bed delete mode 100644 hotspot_coverage/Lung_hotspots.groups delete mode 100644 hotspot_coverage/Melanoma_combined.bed delete mode 100644 hotspot_coverage/Melanoma_combined.groups delete mode 100644 hotspot_coverage/Melanoma_hotspots.bed delete mode 100644 hotspot_coverage/Melanoma_hotspots.groups delete mode 100644 hotspot_coverage/Thyroid_combined.bed delete mode 100644 hotspot_coverage/Thyroid_combined.groups delete mode 100644 hotspot_coverage/Thyroid_genescreen.bed delete mode 100644 hotspot_coverage/Thyroid_genescreen.groups delete mode 100644 hotspot_coverage/Thyroid_hotspots.bed delete mode 100644 hotspot_coverage/Thyroid_hotspots.groups delete mode 100644 hotspot_coverage/Tumour_combined.bed delete mode 100644 hotspot_coverage/Tumour_combined.groups delete mode 100644 hotspot_coverage/Tumour_genescreen.bed delete mode 100644 hotspot_coverage/Tumour_genescreen.groups delete mode 100644 hotspot_coverage/Tumour_hotspots.bed delete mode 100644 hotspot_coverage/Tumour_hotspots.groups delete mode 100644 hotspot_coverage/aitcl_combined.bed delete mode 100644 hotspot_coverage/aitcl_combined.groups delete mode 100644 hotspot_coverage/aitcl_genescreen.bed delete mode 100644 hotspot_coverage/aitcl_genescreen.groups delete mode 100644 hotspot_coverage/aitcl_hotspots.bed delete mode 100644 hotspot_coverage/aitcl_hotspots.groups delete mode 100644 hotspot_coverage/aml_combined.bed delete mode 100644 hotspot_coverage/aml_combined.groups delete mode 100644 hotspot_coverage/aml_genescreen.bed delete mode 100644 hotspot_coverage/aml_genescreen.groups delete mode 100644 hotspot_coverage/breast_combined.bed delete mode 100644 hotspot_coverage/breast_combined.groups delete mode 100644 hotspot_coverage/breast_hotspots.bed delete mode 100644 hotspot_coverage/breast_hotspots.groups delete mode 100644 hotspot_coverage/cll_combined.bed delete mode 100644 hotspot_coverage/cll_combined.groups delete mode 100644 hotspot_coverage/cll_genescreen.bed delete mode 100644 hotspot_coverage/cll_genescreen.groups delete mode 100644 hotspot_coverage/endometrial-pole-tp53_combined.bed delete mode 100644 hotspot_coverage/endometrial-pole-tp53_combined.groups delete mode 100644 hotspot_coverage/endometrial-pole-tp53_genescreen.bed delete mode 100644 hotspot_coverage/endometrial-pole-tp53_genescreen.groups delete mode 100644 hotspot_coverage/endometrial-pole-tp53_hotspots.bed delete mode 100644 hotspot_coverage/endometrial-pole-tp53_hotspots.groups delete mode 100644 hotspot_coverage/endometrial-pole_combined.bed delete mode 100644 hotspot_coverage/endometrial-pole_combined.groups delete mode 100644 hotspot_coverage/endometrial-pole_genescreen.bed delete mode 100644 hotspot_coverage/endometrial-pole_genescreen.groups delete mode 100644 hotspot_coverage/endometrial-pole_hotspots.bed delete mode 100644 hotspot_coverage/endometrial-pole_hotspots.groups delete mode 100644 hotspot_coverage/fight-209_combined.bed delete mode 100644 hotspot_coverage/fight-209_combined.groups delete mode 100644 hotspot_coverage/fight-209_hotspots.bed delete mode 100644 hotspot_coverage/fight-209_hotspots.groups delete mode 100644 hotspot_coverage/mpn_combined.bed delete mode 100644 hotspot_coverage/mpn_combined.groups delete mode 100644 hotspot_coverage/mpn_genescreen.bed delete mode 100644 hotspot_coverage/mpn_genescreen.groups delete mode 100644 hotspot_coverage/myeloid_combined.bed delete mode 100644 hotspot_coverage/myeloid_combined.groups delete mode 100644 hotspot_coverage/myeloid_genescreen.bed delete mode 100644 hotspot_coverage/myeloid_genescreen.groups delete mode 100644 hotspot_variants/Colorectal.bed delete mode 100644 hotspot_variants/GIST.bed delete mode 100644 hotspot_variants/Glioma.bed delete mode 100644 hotspot_variants/Lung.bed delete mode 100644 hotspot_variants/Melanoma.bed delete mode 100644 hotspot_variants/Thyroid.bed delete mode 100644 hotspot_variants/Tumour.bed delete mode 100644 hotspot_variants/aitcl.bed delete mode 100644 hotspot_variants/aml.bed delete mode 100755 hotspot_variants/breast.bed delete mode 100644 hotspot_variants/cll.bed delete mode 100644 hotspot_variants/endometrial-pole-tp53.bed delete mode 100644 hotspot_variants/endometrial-pole.bed delete mode 100644 hotspot_variants/fight-209.bed delete mode 100644 hotspot_variants/mpn.bed delete mode 100644 hotspot_variants/myeloid.bed delete mode 100755 preferred_transcripts.txt delete mode 100644 rerun_coverage.sh delete mode 100644 scripts/call_extra_padding_variants.sh delete mode 100755 scripts/coverage2json.py delete mode 100644 scripts/filter_extra_padding_variants.py delete mode 100755 scripts/gather_list.py delete mode 100644 scripts/keep_blacklisted_variants.py delete mode 100755 scripts/tsv2db.py delete mode 100755 tests/test_data_tsv2db/NTC_fake_variants.tsv delete mode 100755 tests/test_data_tsv2db/NTC_no_var.tsv delete mode 100755 tests/test_data_tsv2db/NTC_novar_blanks.tsv delete mode 100755 tests/test_data_tsv2db/sample_CombinedVariantOutput.tsv delete mode 100755 tests/test_data_tsv2db/sample_CombinedVariantOutput_blanks.tsv delete mode 100755 tests/test_data_tsv2db/sample_CombinedVariantOutput_novar.tsv delete mode 100755 tests/test_tsv2db.py delete mode 100644 vendorCaptureBed_100pad_updated.bed diff --git a/2_TSO500.sh b/2_TSO500.sh index 40ae7e7..b0b4c06 100755 --- a/2_TSO500.sh +++ b/2_TSO500.sh @@ -6,9 +6,8 @@ #SBATCH --partition=high #SBATCH --cpus-per-task=24 -# Description: Run Illumina TSO500 app for each sample then run postprocessing steps - FastQC, -# GATK depth of coverage, coverage calculator, bed2hgvs, gather QC metrics. Kick -# off script 3 when all samples completed +# Description: Run Illumina TSO500 app for each sample then run postprocessing steps for RNA only. +# Kick off script 3 when all samples completed # Use: from /Output/results//TSO500/ directory, for each sample run: # sbatch --export=raw_data=/data/raw/novaseq/,sample_id= 2_TSO500.sh # Version: 1.0.15 @@ -40,15 +39,6 @@ module load anaconda # catch fails early and terminate set -euo pipefail -# define pipeline variables -minimum_coverage="270 135" -coverage_bed_files_path="$pipeline_dir"/hotspot_coverage -vendor_capture_bed="$pipeline_dir"/vendorCaptureBed_100pad_updated.bed -preferred_transcripts="$pipeline_dir"/preferred_transcripts.txt -worksheet=$(grep "$sample_id" SampleSheet_updated.csv | cut -d, -f2) -dna_or_rna=$(grep ${sample_id}, SampleSheet_updated.csv | cut -d, -f9) - - ############################################################################################## # Illumina app ############################################################################################## @@ -99,210 +89,6 @@ for fastqPair in $(find $fastq_path -name *.fastq.gz -type f -printf "%f\n" | cu done -############################################################################################## -# DNA only steps -############################################################################################## - -if [ "$dna_or_rna" = "DNA" ]; then - - - #------------------------------------------------------------------------------------- - # Call variants outside of app ROI - #------------------------------------------------------------------------------------- - - bash "$pipeline_scripts"/call_extra_padding_variants.sh "$sample_id" "$pipeline_version" - - - #------------------------------------------------------------------------------------- - # Run depth of coverage with limited bed (whole 500 takes a long time) - #------------------------------------------------------------------------------------- - - # set and make filepaths for depth of coverage - bam_path="$output_path"/Logs_Intermediates/StitchedRealigned/"$sample_id"/ - depth_path="$output_path"/depth_of_coverage - mkdir -p $depth_path - - # reheader the bams to local area - java -jar /Apps/wren/picard/2.21.6/bin/picard.jar AddOrReplaceReadGroups \ - I="$bam_path"/"$sample_id".bam \ - O="$bam_path"/"$sample_id"_add_rg.bam \ - RGID=4 \ - RGLB=lib1 \ - RGPL=ILLUMINA \ - RGPU=unit1 \ - RGSM=20 - - # index new bam - samtools index "$bam_path"/"$sample_id"_add_rg.bam "$bam_path"/"$sample_id"_add_rg.bam.bai - - # run depth of coverage - gatk DepthOfCoverage \ - -I "$bam_path"/"$sample_id"_add_rg.bam \ - -L "$vendor_capture_bed" \ - -R "$app_dir"/resources/genomes/hg19_hardPAR/genome.fa \ - -O "$depth_path"/"$sample_id"_depth_of_coverage - - # change to tab delimited and remove colon from column 1 - sed 's/:/\t/g' "$depth_path"/"$sample_id"_depth_of_coverage \ - | sed 's/,/\t/g' | grep -v 'Locus' \ - | sort -k1,1 -k2,2n | bgzip \ - > "$depth_path"/"$sample_id"_depth_of_coverage.gz - - # tabix index depth of coverage file - tabix \ - -b 2 \ - -e 2 \ - -s 1 \ - "$depth_path"/"$sample_id"_depth_of_coverage.gz - - # deactivate env - set +u - conda deactivate - set -u - - - #------------------------------------------------------------------------------------- - # Run coverage calculator at 135X and 270X depth cutoffs - #------------------------------------------------------------------------------------- - - # repeat for each coverage value - for min_coverage in $minimum_coverage; do - - # activate coverage calculator conda env - set +u - conda activate CoverageCalculatorPy - set -u - - # set output directory for coverage files - hscov_outdir=hotspot_coverage_"$min_coverage"x - - # run coverage calculator on each bed file - for bed_file in "$coverage_bed_files_path"/*.bed; do - - name=$(echo $(basename $bed_file) | cut -d"." -f1) - - python /data/diagnostics/apps/CoverageCalculatorPy/CoverageCalculatorPy-v1.1.0/CoverageCalculatorPy.py \ - -B "$coverage_bed_files_path"/"$name".bed \ - -D "$depth_path"/"$sample_id"_depth_of_coverage.gz \ - --depth "$min_coverage" \ - --padding 0 \ - --groupfile "$coverage_bed_files_path"/"$name".groups \ - --outname "$sample_id"_"$name" \ - --outdir "$depth_path"/"$hscov_outdir"/ - - # remove header from gaps file - if [[ $(wc -l < "$depth_path"/"$hscov_outdir"/"$sample_id"_"$name".gaps) -eq 1 ]]; then - # no gaps - touch "$depth_path"/"$hscov_outdir"/"$sample_id"_"$name".nohead.gaps - - else - # gaps - grep -v '^#' "$depth_path"/"$hscov_outdir"/"$sample_id"_"$name".gaps > "$depth_path"/"$hscov_outdir"/"$sample_id"_"$name".nohead.gaps - - fi - - # remove chr from bed file so bed2hgvs works - cat "$depth_path"/"$hscov_outdir"/"$sample_id"_"$name".nohead.gaps | sed 's/^chr//' > "$depth_path"/"$hscov_outdir"/"$sample_id"_"$name".nohead_nochr.gaps - - # remove intermediate files - rm "$depth_path"/"$hscov_outdir"/"$sample_id"_"$name".gaps - rm "$depth_path"/"$hscov_outdir"/"$sample_id"_"$name".nohead.gaps - - done - - - #------------------------------------------------------------------------------------- - # Run bed2hgvs to add hgvs nomenclature to gaps - #------------------------------------------------------------------------------------- - - # activate bed2hgvs conda env - set +u - conda deactivate - conda activate bed2hgvs - set -u - - # run on each bed file - for gaps_file in "$depth_path"/"$hscov_outdir"/*.nohead_nochr.gaps; do - - name=$(echo $(basename $gaps_file) | cut -d"." -f1) - echo $name - - Rscript /data/diagnostics/apps/bed2hgvs/bed2hgvs-v0.3.0/bed2hgvs.R \ - --bedfile $gaps_file \ - --outname "$name".gaps \ - --outdir "$depth_path"/"$hscov_outdir" \ - --preferred_tx $preferred_transcripts - - # remove intermediate file - rm "$depth_path"/"$hscov_outdir"/"$name".nohead_nochr.gaps - done - - # combine all total coverage files - if [ -f "$depth_path"/"$hscov_outdir"/"$sample_id"_coverage.txt ]; then rm "$depth_path"/"$hscov_outdir"/"$sample_id"_coverage.txt; fi - cat "$depth_path"/"$hscov_outdir"/*.totalCoverage | grep "FEATURE" | head -n 1 >> "$depth_path"/"$hscov_outdir"/"$sample_id"_coverage.txt - cat "$depth_path"/"$hscov_outdir"/*.totalCoverage | grep -v "FEATURE" | grep -vP "combined_\\S+_GENE" >> "$depth_path"/"$hscov_outdir"/"$sample_id"_coverage.txt - - # deactivate env - set +u - conda deactivate - set -u - - - #------------------------------------------------------------------------------------- - # Cosmic gaps - #------------------------------------------------------------------------------------- - - # activate conda env - set +u - conda activate TSO500_post_processing - set -u - - cosmic_tool_path=/data/diagnostics/apps/cosmic_gaps/cosmic_gaps-master - - # parse referral - must be in DNA loop - referral=$(grep "$sample_id" samples_correct_order_"$worksheet"_DNA.csv | cut -d, -f4) - gaps_file="$depth_path"/"$hscov_outdir"/"$sample_id"_"$referral"_hotspots.gaps - - # hotspot gaps file may be missing for some referrals - if [[ -f $gaps_file ]] - then - - # only run bedtools intersect for certain referral types - if [ $referral = "Melanoma" ] || [ $referral = "Lung" ] || [ $referral = "Colorectal" ] || [ $referral = "GIST" ] || [ $referral = "breast" ] - then - dos2unix $gaps_file - - # find the overlap between the hotspots file and the referral file from cosmic - bedtools intersect \ - -loj \ - -F 1 \ - -a $gaps_file \ - -b "$cosmic_tool_path"/cosmic_bedfiles/"$referral".bed \ - -wao \ - > "$depth_path"/"$hscov_outdir"/"$sample_id"_"$referral"_intersect.txt - - fi - - # filter the output - python "$cosmic_tool_path"/filter_table.py \ - --sampleId $sample_id \ - --referral $referral \ - --gaps_path "$depth_path"/"$hscov_outdir"/ \ - --bedfile_path "$cosmic_tool_path"/cosmic_bedfiles/ - - fi - - # deactivate env - set +u - conda deactivate - set -u - - done - -fi - - - ############################################################################################## # Gather QC metrics for sample ############################################################################################## @@ -334,54 +120,15 @@ done # pull out metrics from the Illumina app MetricsOutput.tsv completed_all_steps=$(grep COMPLETED_ALL_STEPS analysis/"$sample_id"/Results/MetricsOutput.tsv | cut -f2) -# DNA only metrics -if [ "$dna_or_rna" = "DNA" ]; then - - contamination_score=$(grep CONTAMINATION_SCORE analysis/"$sample_id"/Results/MetricsOutput.tsv | cut -f4) - contamination_p_value=$(grep CONTAMINATION_P_VALUE analysis/"$sample_id"/Results/MetricsOutput.tsv | cut -f4) - total_pf_reads=$(grep TOTAL_PF_READS analysis/"$sample_id"/Results/MetricsOutput.tsv | head -n1 | cut -f4) - median_insert_size=$(grep MEDIAN_INSERT_SIZE analysis/"$sample_id"/Results/MetricsOutput.tsv | head -n1 | cut -f4) - median_exon_coverage=$(grep MEDIAN_EXON_COVERAGE analysis/"$sample_id"/Results/MetricsOutput.tsv | cut -f4) - pct_exon_50x=$(grep PCT_EXON_50X analysis/"$sample_id"/Results/MetricsOutput.tsv | cut -f4) - - contamination_pass_fail=PASS - if [ $contamination_score -gt 3106 ]; then - - # use python to handle float - p_value_cutoff=$(python -c "print(float("$contamination_p_value") > 0.049)") - if [ $p_value_cutoff = "True" ]; then - contamination_pass_fail=FAIL - fi - fi - - - #run samtools to get the number of reads in the bam file - if [[ -f ./analysis/"$sample_id"/Logs_Intermediates/StitchedRealigned/"$sample_id"/"$sample_id".bam ]]; then - reads=$( samtools view -c ./analysis/"$sample_id"/Logs_Intermediates/StitchedRealigned/"$sample_id"/"$sample_id".bam ) - else - reads="NA" - fi - - # add to sample QC file - echo -e "Sample\tFastQC\tcompleted_all_steps\tcontamination_pass_fail\tcontamination_score\tcontamination_p_value\ttotal_pf_reads\tmedian_insert_size\tmedian_exon_coverage\tpct_exon_50x\tAligned_reads" > "$output_path"/"$sample_id"_"$dna_or_rna"_QC.txt - echo -e "$sample_id\t$fastqc_status\t$completed_all_steps\t$contamination_pass_fail\t$contamination_score\t$contamination_p_value\t$total_pf_reads\t$median_insert_size\t$median_exon_coverage\t$pct_exon_50x\t$reads" >> "$output_path"/"$sample_id"_"$dna_or_rna"_QC.txt - -fi - - # RNA only metrics -if [ "$dna_or_rna" = "RNA" ]; then - - median_cv_gene_500x=$(grep "MEDIAN_CV_GENE_500X" analysis/"$sample_id"/Results/MetricsOutput.tsv | cut -f4) - total_on_target_reads=$(grep "TOTAL_ON_TARGET_READS" analysis/"$sample_id"/Results/MetricsOutput.tsv | tail -n1 | cut -f4) - median_insert_size=$(grep "MEDIAN_INSERT_SIZE" analysis/"$sample_id"/Results/MetricsOutput.tsv | tail -n1 | cut -f4) - total_pf_reads=$(grep "TOTAL_PF_READS" analysis/"$sample_id"/Results/MetricsOutput.tsv | tail -n1 | cut -f4) - - # add to sample QC file - echo -e "Sample\tFastQC\tcompleted_all_steps\tmedian_cv_gene_500x\ttotal_on_target_reads\tmedian_insert_size\ttotal_pf_reads" > "$output_path"/"$sample_id"_"$dna_or_rna"_QC.txt - echo -e "$sample_id\t$fastqc_status\t$completed_all_steps\t$median_cv_gene_500x\t$total_on_target_reads\t$median_insert_size\t$total_pf_reads" >> "$output_path"/"$sample_id"_"$dna_or_rna"_QC.txt - -fi +median_cv_gene_500x=$(grep "MEDIAN_CV_GENE_500X" analysis/"$sample_id"/Results/MetricsOutput.tsv | cut -f4) +total_on_target_reads=$(grep "TOTAL_ON_TARGET_READS" analysis/"$sample_id"/Results/MetricsOutput.tsv | tail -n1 | cut -f4) +median_insert_size=$(grep "MEDIAN_INSERT_SIZE" analysis/"$sample_id"/Results/MetricsOutput.tsv | tail -n1 | cut -f4) +total_pf_reads=$(grep "TOTAL_PF_READS" analysis/"$sample_id"/Results/MetricsOutput.tsv | tail -n1 | cut -f4) + +# add to sample QC file +echo -e "Sample\tFastQC\tcompleted_all_steps\tmedian_cv_gene_500x\ttotal_on_target_reads\tmedian_insert_size\ttotal_pf_reads" > "$output_path"/"$sample_id"_RNA_QC.txt +echo -e "$sample_id\t$fastqc_status\t$completed_all_steps\t$median_cv_gene_500x\t$total_on_target_reads\t$median_insert_size\t$total_pf_reads" >> "$output_path"/"$sample_id"_RNA_QC.txt ############################################################################################## diff --git a/TSO_extra_padding_chr.interval_list b/TSO_extra_padding_chr.interval_list deleted file mode 100644 index 8ec7646..0000000 --- a/TSO_extra_padding_chr.interval_list +++ /dev/null @@ -1,714 +0,0 @@ -chr1 27022889 27022892 ARID1A(NM_0060154):c-6 -chr1 27024033 27024036 ARID1A(NM_0060154):c1137+5 -chr1 27056136 27056139 ARID1A(NM_0060154):c1138-5 -chr1 27056356 27056359 ARID1A(NM_0060154):c1350+5 -chr1 27057637 27057640 ARID1A(NM_0060154):c1351-5 -chr1 27058097 27058100 ARID1A(NM_0060154):c1803+5 -chr1 27059161 27059164 ARID1A(NM_0060154):c1804-5 -chr1 27059285 27059288 ARID1A(NM_0060154):c1920+5 -chr1 27087341 27087344 ARID1A(NM_0060154):c1921-5 -chr1 27087589 27087592 ARID1A(NM_0060154):c2161+5 -chr1 27087869 27087872 ARID1A(NM_0060154):c2162-5 -chr1 27087966 27087969 ARID1A(NM_0060154):c2251+5 -chr1 27088637 27088640 ARID1A(NM_0060154):c2252-5 -chr1 27088812 27088815 ARID1A(NM_0060154):c2419+5 -chr1 27089458 27089461 ARID1A(NM_0060154):c2420-5 -chr1 27089778 27089781 ARID1A(NM_0060154):c2732+5 -chr1 27092706 27092709 ARID1A(NM_0060154):c2733-5 -chr1 27092859 27092862 ARID1A(NM_0060154):c2878+5 -chr1 27092942 27092945 ARID1A(NM_0060154):c2879-5 -chr1 27093059 27093062 ARID1A(NM_0060154):c2988+5 -chr1 27094275 27094278 ARID1A(NM_0060154):c2989-5 -chr1 27094492 27094495 ARID1A(NM_0060154):c3198+5 -chr1 27097604 27097607 ARID1A(NM_0060154):c3199-5 -chr1 27097819 27097822 ARID1A(NM_0060154):c3406+5 -chr1 27098985 27098988 ARID1A(NM_0060154):c3407-5 -chr1 27099125 27099128 ARID1A(NM_0060154):c3539+5 -chr1 27099297 27099300 ARID1A(NM_0060154):c3540-5 -chr1 27099480 27099483 ARID1A(NM_0060154):c3715+5 -chr1 27099831 27099834 ARID1A(NM_0060154):c3716-5 -chr1 27099989 27099992 ARID1A(NM_0060154):c3866+5 -chr1 27100065 27100068 ARID1A(NM_0060154):c3867-5 -chr1 27100210 27100213 ARID1A(NM_0060154):c4004+5 -chr1 27100287 27100290 ARID1A(NM_0060154):c4005-5 -chr1 27100391 27100394 ARID1A(NM_0060154):c4101+5 -chr1 27100814 27100817 ARID1A(NM_0060154):c4102-5 -chr1 27101713 27101716 ARID1A(NM_0060154):c4993+5 -chr1 27102062 27102065 ARID1A(NM_0060154):c4994-5 -chr1 27102200 27102203 ARID1A(NM_0060154):c5124+5 -chr1 27105508 27105511 ARID1A(NM_0060154):c5125-5 -chr1 27107249 27107252 ARID1A(NM_0060154):c*5 -chr1 43814928 43814931 MPL(NM_005373.2):exon_10_start -chr1 43815032 43815035 MPL(NM_005373.2):exon_10_end -chr1 115252184 115252187 NRAS(NM_0025243):c450+6 -chr1 115252351 115252354 NRAS(NM_0025243):cc -chr1 115256415 115256418 NRAS(NM_0025243):c290+6 -chr1 115256521 115256524 NRAS(NM_002524.4):codon_61_start -chr1 115256533 115256536 NRAS(NM_002524.4):codon_61_end -chr1 115256601 115256604 NRAS(NM_0025243):cc -chr1 115258665 115258668 NRAS(NM_0025243):c111+6 -chr1 115258736 115258739 NRAS(NM_002524.4):codons_12-13_start -chr1 115258751 115258754 NRAS(NM_002524.4):codons_12-13_end -chr1 115258783 115258786 NRAS(NM_0025243):cc -chr1 226252024 226252027 H3F3A(NM_0021074):c-23-6 -chr1 226252182 226252185 H3F3A(NM_0021074):c128+5 -chr2 25457142 25457145 DNMT3A(NM_175629.2):exon_23_start -chr2 25457291 25457294 DNMT3A(NM_175629.2):exon_23_end -chr2 25458570 25458573 DNMT3A(NM_175629.2):exon_22_start -chr2 25458696 25458699 DNMT3A(NM_175629.2):exon_22_end -chr2 25459799 25459802 DNMT3A(NM_175629.2):exon_21_start -chr2 25459876 25459879 DNMT3A(NM_175629.2):exon_21_end -chr2 25461993 25461996 DNMT3A(NM_175629.2):exon_20_start -chr2 25462086 25462089 DNMT3A(NM_175629.2):exon_20_end -chr2 25463165 25463168 DNMT3A(NM_175629.2):exon_19_start -chr2 25463321 25463324 DNMT3A(NM_175629.2):exon_19_end -chr2 25463503 25463506 DNMT3A(NM_175629.2):exon_18_start -chr2 25463601 25463604 DNMT3A(NM_175629.2):exon_18_end -chr2 25464425 25464428 DNMT3A(NM_175629.2):exon_17_start -chr2 25464578 25464581 DNMT3A(NM_175629.2):exon_17_end -chr2 25466761 25466764 DNMT3A(NM_175629.2):exon_16_start -chr2 25466853 25466856 DNMT3A(NM_175629.2):exon_16_end -chr2 25467018 25467021 DNMT3A(NM_175629.2):exon_15_start -chr2 25467209 25467212 DNMT3A(NM_175629.2):exon_15_end -chr2 25467403 25467406 DNMT3A(NM_175629.2):exon_14_start -chr2 25467523 25467526 DNMT3A(NM_175629.2):exon_14_end -chr2 25468116 25468119 DNMT3A(NM_175629.2):exon_13_start -chr2 25468203 25468206 DNMT3A(NM_175629.2):exon_13_end -chr2 25468883 25468886 DNMT3A(NM_175629.2):exon_12_start -chr2 25468935 25468938 DNMT3A(NM_175629.2):exon_12_end -chr2 25469023 25469026 DNMT3A(NM_175629.2):exon_11_start -chr2 25469180 25469183 DNMT3A(NM_175629.2):exon_11_end -chr2 25469483 25469486 DNMT3A(NM_175629.2):exon_10_start -chr2 25469647 25469650 DNMT3A(NM_175629.2):exon_10_end -chr2 25469914 25469917 DNMT3A(NM_175629.2):exon_9_start -chr2 25470029 25470032 DNMT3A(NM_175629.2):exon_9_end -chr2 25470454 25470457 DNMT3A(NM_175629.2):exon_8_start -chr2 25470620 25470623 DNMT3A(NM_175629.2):exon_8_end -chr2 25470900 25470903 DNMT3A(NM_175629.2):exon_7_start -chr2 25471123 25471126 DNMT3A(NM_175629.2):exon_7_end -chr2 25472521 25472598 DNMT3A(NM_153759.3):exon_2 -chr2 25475058 25475071 DNMT3A(NM_153759.3):exon_1 -chr2 25497804 25497807 DNMT3A(NM_175629.2):exon_6_start -chr2 25497958 25497961 DNMT3A(NM_175629.2):exon_6_end -chr2 25498363 25498366 DNMT3A(NM_175629.2):exon_5_start -chr2 25498414 25498417 DNMT3A(NM_175629.2):exon_5_end -chr2 25505304 25505307 DNMT3A(NM_175629.2):exon_4_start -chr2 25505582 25505585 DNMT3A(NM_175629.2):exon_4_end -chr2 25523002 25523005 DNMT3A(NM_175629.2):exon_3_start -chr2 25523114 25523117 DNMT3A(NM_175629.2):exon_3_end -chr2 25536776 25536779 DNMT3A(NM_175629.2):exon_2_start -chr2 25536855 25536858 DNMT3A(NM_175629.2):exon_2_end -chr2 198266460 198266463 SF3B1(NM_012433.3):exon_16_start -chr2 198266614 198266617 SF3B1(NM_012433.3):exon_16_end -chr2 198266703 198266706 SF3B1(NM_012433.3):exon_15_start -chr2 198266856 198266859 SF3B1(NM_012433.3):exon_15_end -chr2 198267274 198267277 SF3B1(NM_012433.3):exon_14_start -chr2 198267552 198267555 SF3B1(NM_012433.3):exon_14_end -chr2 198267667 198267670 SF3B1(NM_012433.3):exon_13_start -chr2 198267761 198267764 SF3B1(NM_012433.3):exon_13_end -chr2 209113087 209113090 IDH2(NM_0058962):c414+6 -chr2 209113104 209113107 IDH1(NM_005896.3):codon_R132_start -chr2 209113116 209113119 IDH1(NM_005896.3):codon_R132_end -chr2 209113386 209113389 IDH2(NM_0058962):cc -chr3 49412862 49412864 RHOA(NM001664.3):exon_2_start -chr3 49413025 49413027 RHOA(NM001664.3):exon_2_end -chr3 128199856 128199859 GATA2(NM_032638.4):exon_7_start -chr3 128200163 128200166 GATA2(NM_032638.4):exon_7_end -chr3 128200656 128200659 GATA2(NM_032638.4):exon_6_start -chr3 128200789 128200792 GATA2(NM_032638.4):exon_6_end -chr3 128202697 128202700 GATA2(NM_032638.4):exon_5_start -chr3 128202850 128202853 GATA2(NM_032638.4):exon_5_end -chr3 128204564 128204567 GATA2(NM_032638.4):exon_4_start -chr3 128205213 128205216 GATA2(NM_032638.4):exon_4_end -chr3 128205640 128205643 GATA2(NM_032638.4):exon_3_start -chr3 128205876 128205879 GATA2(NM_032638.4):exon_3_end -chr3 178927969 178927971 PIK3CA(NM_0062182):exon_8_start -chr3 178928129 178928131 PIK3CA(NM_0062182):exon_8_end -chr3 178935993 178935995 PIK3CA(NM_0062182):exon_10_start -chr3 178936125 178936127 PIK3CA(NM_0062182):exon_10_end -chr3 178951877 178951879 PIK3CA(NM_0062182):exon_21_start -chr3 178952155 178952157 PIK3CA(NM_0062182):exon_21_end -chr4 1803246 1803248 FGFR3(NM_000142.4):codon_R200 -chr4 1803564 1803566 FGFR3(NM_000142.4):codon_R248 -chr4 1803567 1803569 FGFR3(NM_000142.4):codon_S249 -chr4 1805512 1805514 FGFR3(NM_000142.4):codon_G342 -chr4 1806057 1806247 FGFR3(NM_000142.4):exon_9 -chr4 1807333 1807335 FGFR3(NM_000142.4):codon_M528 -chr4 1807369 1807371 FGFR3(NM_000142.4):codon_N540 -chr4 1807494 1807496 FGFR3(NM_000142.4):codon_V555 -chr4 1807802 1807804 FGFR3(NM_000142.4):codon_R621 -chr4 1807862 1807864 FGFR3(NM_000142.4):codon_D641 -chr4 1807889 1807891 FGFR3(NM_000142.4):codon_K650 -chr4 55141002 55141005 PDGFRA(NM_0062064):c1654-5 -chr4 55141002 55141005 PDGFRA(NM_006206.5):exon_12_start -chr4 55141142 55141145 PDGFRA(NM_0062064):c1786+5 -chr4 55141142 55141145 PDGFRA(NM_006206.5):exon_12_end -chr4 55144057 55144060 PDGFRA(NM_0062064):c1892-5 -chr4 55144057 55144060 PDGFRA(NM_006206.5):exon_14_start -chr4 55144175 55144178 PDGFRA(NM_0062064):c2002+5 -chr4 55144175 55144178 PDGFRA(NM_006206.5):exon_14_end -chr4 55152002 55152005 PDGFRA(NM_0062064):c2440-5 -chr4 55152002 55152005 PDGFRA(NM_006206.5):exon_18_start -chr4 55152132 55152135 PDGFRA(NM_006206.5):exon_18_end -chr4 55152132 55152135 PDGFRA(NM_0062064):c2562+5 -chr4 55592017 55592020 KIT(NM_0002222):c1347-5 -chr4 55592218 55592221 KIT(NM_0002222):c1540+5 -chr4 55593576 55593579 KIT(NM_0002222):c1648-5 -chr4 55593710 55593713 KIT(NM_0002222):c1774+5 -chr4 55594171 55594174 KIT(NM_0002222):c1880-5 -chr4 55594289 55594292 KIT(NM_0002222):c1990+5 -chr4 55595495 55595498 KIT(NM_0002222):c1991-5 -chr4 55595653 55595656 KIT(NM_0002222):c2141+5 -chr4 55599230 55599233 KIT(NM_0002222):c2362-5 -chr4 55599230 55599233 KIT(NM_000222.2):exon_17_start -chr4 55599360 55599363 KIT(NM_0002222):c2484+5 -chr4 55599360 55599363 KIT(NM_000222.2):exon_17_end -chr4 106155094 106155097 TET2(NM_001127208.2):exon_3_start -chr4 106158599 106158602 TET2(NM_001127208.2):exon_3_end -chr4 106162490 106162493 TET2(NM_001127208.2):exon_4_start -chr4 106162588 106162591 TET2(NM_001127208.2):exon_4_end -chr4 106163985 106163988 TET2(NM_001127208.2):exon_5_start -chr4 106164086 106164089 TET2(NM_001127208.2):exon_5_end -chr4 106164721 106164724 TET2(NM_001127208.2):exon_6_start -chr4 106164937 106164940 TET2(NM_001127208.2):exon_6_end -chr4 106180770 106180773 TET2(NM_001127208.2):exon_7_start -chr4 106180928 106180931 TET2(NM_001127208.2):exon_7_end -chr4 106182910 106182913 TET2(NM_001127208.2):exon_8_start -chr4 106183007 106183010 TET2(NM_001127208.2):exon_8_end -chr4 106190761 106190764 TET2(NM_001127208.2):exon_9_start -chr4 106190906 106190909 TET2(NM_001127208.2):exon_9_end -chr4 106193715 106193718 TET2(NM_001127208.2):exon_10_start -chr4 106194077 106194080 TET2(NM_001127208.2):exon_10_end -chr4 106196199 106196202 TET2(NM_001127208.2):exon_11_start -chr4 106197678 106197681 TET2(NM_001127208.2):exon_11_end -chr5 1295225 1295228 TERT(NM_1982532):c-124 -chr5 1295227 1295230 TERT(NM_1982532):c-124 -chr5 1295247 1295250 TERT(NM_1982532):c-146 -chr5 1295249 1295252 TERT(NM_1982532):c-146 -chr5 170837525 170837528 NPM1(NM_002520.6):exon_11_start -chr5 170837571 170837574 NPM1(NM_002520.6):exon_11_end -chr6 152265302 152265305 ESR1(NM_0001253):c761-6 -chr6 152265645 152265648 ESR1(NM_0001253):cc -chr6 152332785 152332788 ESR1(NM_0001253):c1097-6 -chr6 152332931 152332934 ESR1(NM_0001253):cc -chr6 152415514 152415517 ESR1(NM_0001253):c1370-6 -chr6 152415635 152415638 ESR1(NM_0001253):cc -chr6 152419861 152419864 ESR1(NM_0001253):c1554-6 -chr6 152420103 152420106 ESR1(NM_0001253):cc -chr7 55241608 55241611 EGFR(NM_0052283):c2062-5 -chr7 55241738 55241741 EGFR(NM_0052283):c2184+5 -chr7 55242409 55242412 EGFR(NM_0052283):c2185-5 -chr7 55242515 55242518 EGFR(NM_0052283):c2283+5 -chr7 55248980 55248983 EGFR(NM_0052283):c2284-5 -chr7 55249173 55249176 EGFR(NM_0052283):c2469+5 -chr7 55259406 55259409 EGFR(NM_0052283):c2470-5 -chr7 55259569 55259572 EGFR(NM_0052283):c2625+5 -chr7 116411546 116411549 MET(NM_0011275001):c2785-5 -chr7 116414931 116414934 MET(NM_0011275001):c3083-1 -chr7 140453069 140453072 BRAF(NM_0043334):c1742-5 -chr7 140453195 140453198 BRAF(NM_0043334):c1860+5 -chr7 140481370 140481373 BRAF(NM_0043334):c1315-5 -chr7 140481495 140481498 BRAF(NM_0043334):c1432+5 -chr7 148504732 148504735 EZH2(NM_004456.4):exon_20_start -chr7 148504800 148504803 EZH2(NM_004456.4):exon_20_end -chr7 148506157 148506160 EZH2(NM_004456.4):exon_19_start -chr7 148506249 148506252 EZH2(NM_004456.4):exon_19_end -chr7 148506396 148506399 EZH2(NM_004456.4):exon_18_start -chr7 148506484 148506487 EZH2(NM_004456.4):exon_18_end -chr7 148507419 148507422 EZH2(NM_004456.4):exon_17_start -chr7 148507508 148507511 EZH2(NM_004456.4):exon_17_end -chr7 148508711 148508714 EZH2(NM_004456.4):exon_16_start -chr7 148508814 148508817 EZH2(NM_004456.4):exon_16_end -chr7 148511045 148511048 EZH2(NM_004456.4):exon_15_start -chr7 148511231 148511234 EZH2(NM_004456.4):exon_15_end -chr7 148512000 148512003 EZH2(NM_004456.4):exon_14_start -chr7 148512133 148512136 EZH2(NM_004456.4):exon_14_end -chr7 148512592 148512595 EZH2(NM_004456.4):exon_13_start -chr7 148512640 148512643 EZH2(NM_004456.4):exon_13_end -chr7 148513770 148513773 EZH2(NM_004456.4):exon_12_start -chr7 148513872 148513875 EZH2(NM_004456.4):exon_12_end -chr7 148514308 148514311 EZH2(NM_004456.4):exon_11_start -chr7 148514485 148514488 EZH2(NM_004456.4):exon_11_end -chr7 148514963 148514966 EZH2(NM_004456.4):exon_10_start -chr7 148515211 148515214 EZH2(NM_004456.4):exon_10_end -chr7 148516682 148516685 EZH2(NM_004456.4):exon_9_start -chr7 148516781 148516784 EZH2(NM_004456.4):exon_9_end -chr7 148523540 148523543 EZH2(NM_004456.4):exon_8_start -chr7 148523726 148523729 EZH2(NM_004456.4):exon_8_end -chr7 148524250 148524253 EZH2(NM_004456.4):exon_7_start -chr7 148524360 148524363 EZH2(NM_004456.4):exon_7_end -chr7 148525826 148525829 EZH2(NM_004456.4):exon_6_start -chr7 148525974 148525977 EZH2(NM_004456.4):exon_6_end -chr7 148526814 148526817 EZH2(NM_004456.4):exon_5_start -chr7 148526942 148526945 EZH2(NM_004456.4):exon_5_end -chr7 148529720 148529723 EZH2(NM_004456.4):exon_4_start -chr7 148529844 148529847 EZH2(NM_004456.4):exon_4_end -chr7 148543556 148543559 EZH2(NM_004456.4):exon_3_start -chr7 148543692 148543695 EZH2(NM_004456.4):exon_3_end -chr7 148544268 148544271 EZH2(NM_004456.4):exon_2_start -chr7 148544392 148544395 EZH2(NM_004456.4):exon_2_end -chr8 38285493 38285495 FGFR1(NM_023110.2):codon_R189 -chr8 38282207 38282209 FGFR1(NM_023110.2):codon_P252 -chr8 38277213 38277215 FGFR1(NM_023110.2):codon_Y374 -chr8 38277192 38277194 FGFR1(NM_023110.2):codon_C381 -chr8 38275841 38275843 FGFR1(NM_023110.2):codon_R445 -chr8 38274849 38274851 FGFR1(NM_023110.2):codon_N546 -chr8 38273559 38273561 FGFR1(NM_023110.2):codon_V561 -chr8 38272306 38272308 FGFR1(NM_023110.2):codon_K656 -chr9 5069919 5069922 JAK2(NM_004972.3):exon_12_start -chr9 5070054 5070057 JAK2(NM_004972.3):exon_12_end -chr9 5073763 5073766 JAK2(NM_004972.3):codon_V617_start -chr9 5073775 5073778 JAK2(NM_004972.3):codon_V617_end -chr9 21968222 21968225 CDKN2A(NM_0000773):c*6 -chr9 21968243 21968246 CDKN2A(NM_0000773):c458-5 -chr9 21970895 21970898 CDKN2A(NM_0000773):c151-5 -chr9 21971209 21971212 CDKN2A(NM_0000773):c457+5 -chr9 21974671 21974674 CDKN2A(NM_0000773):c150+5 -chr9 21974828 21974831 CDKN2A(NM_0000773):c-5 -chr9 139390517 139390520 NOTCH1(NM_017617.4):exon_34_start -chr9 139392012 139392015 NOTCH1(NM_017617.4):exon_34_end -chr10 43572701 43572704 RET(NM_0209754):c-5 -chr10 43572781 43572784 RET(NM_0209754):c73+5 -chr10 43595901 43595904 RET(NM_0209754):c74-5 -chr10 43596172 43596175 RET(NM_0209754):c337+5 -chr10 43597784 43597787 RET(NM_0209754):c338-5 -chr10 43598079 43598082 RET(NM_0209754):c625+5 -chr10 43600394 43600397 RET(NM_0209754):c626-5 -chr10 43600643 43600646 RET(NM_0209754):c867+5 -chr10 43601818 43601821 RET(NM_0209754):c868-5 -chr10 43602021 43602024 RET(NM_0209754):c1063+5 -chr10 43604473 43604476 RET(NM_0209754):c1064-5 -chr10 43604680 43604683 RET(NM_0209754):c1263+5 -chr10 43606649 43606652 RET(NM_0209754):c1264-5 -chr10 43606915 43606918 RET(NM_0209754):c1522+5 -chr10 43607541 43607544 RET(NM_0209754):c1523-5 -chr10 43607674 43607677 RET(NM_0209754):c1648+5 -chr10 43608295 43608298 RET(NM_0209754):c1649-5 -chr10 43608413 43608416 RET(NM_0209754):c1759+5 -chr10 43608998 43609001 RET(NM_0209754):c1760-5 -chr10 43609125 43609128 RET(NM_0209754):c1879+5 -chr10 43609922 43609925 RET(NM_0209754):c1880-5 -chr10 43610186 43610189 RET(NM_0209754):c2136+5 -chr10 43612026 43612029 RET(NM_0209754):c2137-5 -chr10 43612181 43612184 RET(NM_0209754):c2284+5 -chr10 43613815 43613818 RET(NM_0209754):c2285-5 -chr10 43613930 43613933 RET(NM_0209754):c2392+5 -chr10 43614973 43614976 RET(NM_0209754):c2393-5 -chr10 43615195 43615198 RET(NM_0209754):c2607+5 -chr10 43615523 43615526 RET(NM_0209754):c2608-5 -chr10 43615653 43615656 RET(NM_0209754):c2730+5 -chr10 43617388 43617391 RET(NM_0209754):c2731-5 -chr10 43617466 43617469 RET(NM_0209754):c2801+5 -chr10 43619113 43619116 RET(NM_0209754):c2802-5 -chr10 43619258 43619261 RET(NM_0209754):c2939+5 -chr10 43620325 43620328 RET(NM_0209754):c2940-5 -chr10 43620432 43620435 RET(NM_0209754):c3039+5 -chr10 43622017 43622020 RET(NM_0209754):c3040-5 -chr10 43622172 43622175 RET(NM_0209754):c3187+5 -chr10 43623554 43623557 RET(NM_0209754):c3188-5 -chr10 43623719 43623722 RET(NM_0209754):c*5 -chr10 89624221 89624224 PTEN(NM_0003144):c-6 -chr10 89624307 89624310 PTEN(NM_0003144):c79+5 -chr10 89653776 89653779 PTEN(NM_0003144):c80-5 -chr10 89653868 89653871 PTEN(NM_0003144):c164+5 -chr10 89685264 89685267 PTEN(NM_0003144):c165-5 -chr10 89685316 89685319 PTEN(NM_0003144):c209+5 -chr10 89690797 89690800 PTEN(NM_0003144):c210-5 -chr10 89690848 89690851 PTEN(NM_0003144):c253+5 -chr10 89692764 89692767 PTEN(NM_0003144):c254-5 -chr10 89693010 89693013 PTEN(NM_0003144):c492+5 -chr10 89711869 89711872 PTEN(NM_0003144):c493-5 -chr10 89712018 89712021 PTEN(NM_0003144):c634+5 -chr10 89717604 89717607 PTEN(NM_0003144):c635-5 -chr10 89717778 89717781 PTEN(NM_0003144):c801+5 -chr10 89720645 89720648 PTEN(NM_0003144):c802-5 -chr10 89720877 89720880 PTEN(NM_0003144):c1026+5 -chr10 89725038 89725041 PTEN(NM_0003144):c1027-5 -chr10 89725231 89725234 PTEN(NM_0003144):c*5 -chr10 123310900 123310929 FGFR2(NM_000141.4):exon_5_partial_p167-176 -chr10 123310819 123310821 FGFR2(NM_000141.4):codon_R203 -chr10 123298224 123298226 FGFR2(NM_000141.4):codon_R210 -chr10 123279676 123279678 FGFR2(NM_000141.4):codon_S252 -chr10 123279673 123279675 FGFR2(NM_000141.4):codon_P253 -chr10 123279613 123279666 FGFR2(NM_000141.4):exon_7_partial_p256-273 -chr10 123279496 123279594 FGFR2(NM_000141.4):exon_7_partial_p280-312 -chr10 123276972 123276974 FGFR2(NM_000141.4):codon_A315 -chr10 123276909 123276911 FGFR2(NM_000141.4):codon_D336 -chr10 123276891 123276893 FGFR2(NM_000141.4):codon_C342 -chr10 123276876 123276878 FGFR2(NM_000141.4):codon_S347 -chr10 123276864 123276866 FGFR2(NM_000141.4):codon_S351 -chr10 123276855 123276857 FGFR2(NM_000141.4):codon_S354 -chr10 123274802 123274804 FGFR2(NM_000141.4):codon_S372 -chr10 123274793 123274795 FGFR2(NM_000141.4):codon_Y375 -chr10 123274772 123274774 FGFR2(NM_000141.4):codon_C382 -chr10 123274745 123274747 FGFR2(NM_000141.4):codon_M391 -chr10 123274733 123274735 FGFR2(NM_000141.4):codon_V395 -chr10 123258070 123258072 FGFR2(NM_000141.4):codon_M537 -chr10 123258040 123258042 FGFR2(NM_000141.4):codon_I547 -chr10 123258034 123258036 FGFR2(NM_000141.4):codon_N549 -chr10 123256217 123256219 FGFR2(NM_000141.4):codon_V564 -chr10 123256214 123256216 FGFR2(NM_000141.4):codon_E565 -chr10 123256202 123256204 FGFR2(NM_000141.4):codon_K569 -chr10 123256058 123256060 FGFR2(NM_000141.4):codon_L617 -chr10 123247583 123247585 FGFR2(NM_000141.4):codon_E636 -chr10 123247568 123247570 FGFR2(NM_000141.4):codon_K641 -chr10 123247514 123247516 FGFR2(NM_000141.4):codon_K659 -chr10 123246933 123246935 FGFR2(NM_000141.4):codon_R664 -chr10 123246891 123246893 FGFR2(NM_000141.4):codon_R678 -chr11 533760 533763 NM_0053432(HRAS):c290+6 -chr11 533946 533949 NM_0053432(HRAS):cc -chr11 534206 534209 NM_0053432(HRAS):c111+6 -chr11 534324 534327 NM_0053432(HRAS):cc -chr11 119148870 119148873 CBL(NM_005188.3):exon_8_start -chr11 119149009 119149012 CBL(NM_005188.3):exon_8_end -chr11 119149214 119149217 CBL(NM_005188.3):exon_9_start -chr11 119149425 119149428 CBL(NM_005188.3):exon_9_end -chr12 11803056 11803059 ETV6(NM_001987.4):exon_1_start -chr12 11803096 11803099 ETV6(NM_001987.4):exon_1_end -chr12 11905378 11905381 ETV6(NM_001987.4):exon_2_start -chr12 11905515 11905518 ETV6(NM_001987.4):exon_2_end -chr12 11992068 11992071 ETV6(NM_001987.4):exon_3_start -chr12 11992240 11992243 ETV6(NM_001987.4):exon_3_end -chr12 12006355 12006358 ETV6(NM_001987.4):exon_4_start -chr12 12006497 12006500 ETV6(NM_001987.4):exon_4_end -chr12 12022352 12022355 ETV6(NM_001987.4):exon_5_start -chr12 12022905 12022908 ETV6(NM_001987.4):exon_5_end -chr12 12037373 12037376 ETV6(NM_001987.4):exon_6_start -chr12 12037523 12037526 ETV6(NM_001987.4):exon_6_end -chr12 12038854 12038857 ETV6(NM_001987.4):exon_7_start -chr12 12038962 12038965 ETV6(NM_001987.4):exon_7_end -chr12 12043869 12043872 ETV6(NM_001987.4):exon_8_start -chr12 12043982 12043985 ETV6(NM_001987.4):exon_8_end -chr12 25378542 25378545 KRAS(NM_0049853):c450+6 -chr12 25378709 25378712 KRAS(NM_0049853):cc -chr12 25380162 25380165 KRAS(NM_033360.3):exon_3_start -chr12 25380162 25380165 KRAS(NM_0049853):c290+6 -chr12 25380348 25380351 KRAS(NM_033360.3):exon_3_end -chr12 25380348 25380351 KRAS(NM_0049853):cc -chr12 25398202 25398205 KRAS(NM_033360.3):exon_2_start -chr12 25398202 25398205 KRAS(NM_0049853):c111+6 -chr12 25398320 25398323 KRAS(NM_033360.3):exon_2_end -chr12 25398320 25398323 KRAS(NM_0049853):cc -chr12 133249745 133249747 POLE(NM006231.3):c.1360-5_c.1360-2 -chr12 133249866 133249868 POLE(NM006231.3):c.1473+2_c.1473+5 -chr12 133250156 133250158 POLE(NM006231.3):c.1227-5_c.1227-2 -chr12 133250296 133250298 POLE(NM006231.3):c.1359+2_c.1359+5 -chr12 133251979 133251981 POLE(NM006231.3):c.1107-5_c.1107-2 -chr12 133252106 133252108 POLE(NM006231.3):c.1226+2_c.1226+5 -chr12 133252316 133252318 POLE(NM006231.3):c.1021-5_c.1021-2 -chr12 133252409 133252411 POLE(NM006231.3):c.1106+2_c.1106+5 -chr12 133252675 133252677 POLE(NM006231.3):c.910-5_c.910-2 -chr12 133252793 133252795 POLE(NM006231.3):c.1020+2_c.1020+5 -chr12 133253127 133253129 POLE(NM006231.3):c.802-5_c.802-2 -chr12 133253242 133253244 POLE(NM006231.3):c.909+2_c.909+5 -chr13 28592598 28592601 FLT3(NM_004119.2):exon_20_start -chr13 28592728 28592731 FLT3(NM_004119.2):exon_20_end -chr13 28608018 28608021 FLT3(NM_004119.2):exon_15_start -chr13 28608130 28608133 FLT3(NM_004119.2):exon_15_end -chr13 28608213 28608216 FLT3(NM_004119.2):exon_14_start -chr13 28608353 28608356 FLT3(NM_004119.2):exon_14_end -chr13 28608432 28608435 FLT3(NM_004119.2):exon_13_start -chr13 28608546 28608549 FLT3(NM_004119.2):exon_13_end -chr13 32890577 32890595 BRCA2(NM_0000593):c1-21 -chr13 32890666 32890684 BRCA2(NM_0000593):c67+20 -chr13 32893193 32893211 BRCA2(NM_0000593):c68-20 -chr13 32893464 32893482 BRCA2(NM_0000593):c316+20 -chr13 32899192 32899210 BRCA2(NM_0000593):c317-20 -chr13 32899323 32899341 BRCA2(NM_0000593):c425+20 -chr13 32900217 32900235 BRCA2(NM_0000593):c426-20 -chr13 32900289 32900307 BRCA2(NM_0000593):c475+20 -chr13 32900358 32900376 BRCA2(NM_0000593):c476-20 -chr13 32900421 32900439 BRCA2(NM_0000593):c516+20 -chr13 32900615 32900633 BRCA2(NM_0000593):c517-20 -chr13 32900752 32900770 BRCA2(NM_0000593):c631+20 -chr13 32903559 32903577 BRCA2(NM_0000593):c632-20 -chr13 32903631 32903649 BRCA2(NM_0000593):c681+20 -chr13 32905035 32905053 BRCA2(NM_0000593):c682-20 -chr13 32905169 32905187 BRCA2(NM_0000593):c793+20 -chr13 32906388 32906406 BRCA2(NM_0000593):c794-20 -chr13 32907516 32907534 BRCA2(NM_0000593):c1909+20 -chr13 32910381 32910399 BRCA2(NM_0000593):c1910-20 -chr13 32915335 32915353 BRCA2(NM_0000593):c6841+20 -chr13 32918674 32918692 BRCA2(NM_0000593):c6842-20 -chr13 32918792 32918810 BRCA2(NM_0000593):c6937+20 -chr13 32920943 32920961 BRCA2(NM_0000593):c6938-20 -chr13 32921035 32921053 BRCA2(NM_0000593):c7007+20 -chr13 32928977 32928995 BRCA2(NM_0000593):c7008-20 -chr13 32929427 32929445 BRCA2(NM_0000593):c7435+20 -chr13 32930544 32930562 BRCA2(NM_0000593):c7436-20 -chr13 32930748 32930766 BRCA2(NM_0000593):c7617+20 -chr13 32931858 32931876 BRCA2(NM_0000593):c7618-20 -chr13 32932068 32932086 BRCA2(NM_0000593):c7805+20 -chr13 32936639 32936657 BRCA2(NM_0000593):c7806-20 -chr13 32936832 32936850 BRCA2(NM_0000593):c7976+20 -chr13 32937295 32937313 BRCA2(NM_0000593):c7977-20 -chr13 32937672 32937690 BRCA2(NM_0000593):c8331+20 -chr13 32944518 32944536 BRCA2(NM_0000593):c8332-20 -chr13 32944696 32944714 BRCA2(NM_0000593):c8487+20 -chr13 32945072 32945090 BRCA2(NM_0000593):c8488-20 -chr13 32945239 32945257 BRCA2(NM_0000593):c8632+20 -chr13 32950786 32950804 BRCA2(NM_0000593):c8633-20 -chr13 32950930 32950948 BRCA2(NM_0000593):c8754+20 -chr13 32953433 32953451 BRCA2(NM_0000593):c8755-20 -chr13 32953654 32953672 BRCA2(NM_0000593):c8953+20 -chr13 32953866 32953884 BRCA2(NM_0000593):c8954-20 -chr13 32954052 32954070 BRCA2(NM_0000593):c9117+20 -chr13 32954123 32954141 BRCA2(NM_0000593):c9118-20 -chr13 32954284 32954302 BRCA2(NM_0000593):c9256+20 -chr13 32968805 32968823 BRCA2(NM_0000593):c9257-20 -chr13 32969072 32969090 BRCA2(NM_0000593):c9501+20 -chr13 32971014 32971032 BRCA2(NM_0000593):c9502-20 -chr13 32971183 32971201 BRCA2(NM_0000593):c9648+20 -chr13 32972278 32972296 BRCA2(NM_0000593):c9649-20 -chr13 32972909 32972927 BRCA2(NM_0000593):c*20 -chr15 90631813 90631816 IDH2(NM_0021682):c534+6 -chr15 90631813 90631816 IDH2(NM_002168.3):exon_4_start -chr15 90631981 90631984 IDH2(NM_0021682):cc -chr15 90631981 90631984 IDH2(NM_002168.3):exon_4_end -chr17 7572921 7572924 TP53(NM_000546.5):exon_11_start -chr17 7572921 7572924 TP53(NM_0005464):c1101-5 -chr17 7573010 7573013 TP53(NM_0005464):c*5 -chr17 7573010 7573013 TP53(NM_000546.5):exon_11_end -chr17 7573921 7573924 TP53(NM_0005464):c994-5 -chr17 7573921 7573924 TP53(NM_000546.5):exon_10_start -chr17 7574035 7574038 TP53(NM_000546.5):exon_10_end -chr17 7574035 7574038 TP53(NM_0005464):c1100+5 -chr17 7576524 7576527 TP53(NM_0012766951):c*12+1C>T -chr17 7576531 7576534 TP53(NM_001276695.1):exon_10_start -chr17 7576586 7576589 TP53(NM_001276695.1):exon_10_end -chr17 7576619 7576622 TP53(NM_001276696.1):exon_10_start -chr17 7576659 7576662 TP53(NM_001276696.1):exon_10_end -chr17 7576668 7576671 TP53(NM_0012766951):c(NM -chr17 7576847 7576850 TP53(NM_000546.5):exon_9_start -chr17 7576847 7576850 TP53(NM_0005464):c920-5 -chr17 7576928 7576931 TP53(NM_000546.5):exon_9_end -chr17 7576928 7576931 TP53(NM_0005464):c993+5 -chr17 7577013 7577016 TP53(NM_000546.5):exon_8_start -chr17 7577013 7577016 TP53(NM_0005464):c783-5 -chr17 7577157 7577160 TP53(NM_000546.5):exon_8_end -chr17 7577157 7577160 TP53(NM_0005464):c919+5 -chr17 7577493 7577496 TP53(NM_000546.5):exon_7_start -chr17 7577493 7577496 TP53(NM_0005464):c673-5 -chr17 7577610 7577613 TP53(NM_000546.5):exon_7_end -chr17 7577610 7577613 TP53(NM_0005464):c782+5 -chr17 7578171 7578174 TP53(NM_000546.5):exon_6_start -chr17 7578171 7578174 TP53(NM_0005464):c560-5 -chr17 7578291 7578294 TP53(NM_0005464):c672+5 -chr17 7578291 7578294 TP53(NM_000546.5):exon_6_end -chr17 7578365 7578368 TP53(NM_0005464):c376-5 -chr17 7578365 7578368 TP53(NM_000546.5):exon_5_start -chr17 7578556 7578559 TP53(NM_000546.5):exon_5_end -chr17 7578556 7578559 TP53(NM_0005464):c559+5 -chr17 7579306 7579309 TP53(NM_000546.5):exon_4_start -chr17 7579306 7579309 TP53(NM_0005464):c97-5 -chr17 7579592 7579595 TP53(NM_000546.5):exon_4_end -chr17 7579592 7579595 TP53(NM_0005464):c375+5 -chr17 7579694 7579697 TP53(NM_000546.5):exon_3_start -chr17 7579694 7579697 TP53(NM_0005464):c75-5 -chr17 7579723 7579726 TP53(NM_000546.5):exon_3_end -chr17 7579723 7579726 TP53(NM_0005464):c96+5 -chr17 7579833 7579836 TP53(NM_000546.5):exon_2_start -chr17 7579833 7579836 TP53(NM_0005464):c-28-5 -chr17 7579914 7579917 TP53(NM_000546.5):exon_2_end -chr17 7579942 7579945 TP53(NM_0005464):c74+5 -chr17 37868175 37868178 ERBB2(NM_0044482):c902-6 -chr17 37868302 37868305 ERBB2(NM_0044482):cc -chr17 37879566 37879569 ERBB2(NM_0044482):c1947-6 -chr17 37879712 37879715 ERBB2(NM_0044482):cc -chr17 37880159 37880162 ERBB2(NM_0044482):c2209-6 -chr17 37880265 37880268 ERBB2(NM_0044482):cc -chr17 37880973 37880976 ERBB2(NM_0044482):c2308-6 -chr17 37881166 37881169 ERBB2(NM_0044482):cc -chr17 37881296 37881299 ERBB2(NM_0044482):c2494-6 -chr17 37881459 37881462 ERBB2(NM_0044482):cc -chr17 37881574 37881577 ERBB2(NM_0044482):c2650-6 -chr17 37881657 37881660 ERBB2(NM_0044482):c2725+5 -chr17 41197674 41197692 BRCA1(NM_0072943):c5468-20 -chr17 41197821 41197839 BRCA1(NM_0072943):c*20 -chr17 41199639 41199657 BRCA1(NM_0072943):c5407-20 -chr17 41199722 41199740 BRCA1(NM_0072943):c5467+20 -chr17 41201117 41201135 BRCA1(NM_0072943):c5333-20 -chr17 41201213 41201231 BRCA1(NM_0072943):c5406+20 -chr17 41203059 41203077 BRCA1(NM_0072943):c5278-20 -chr17 41203136 41203154 BRCA1(NM_0072943):c5332+20 -chr17 41209048 41209066 BRCA1(NM_0072943):c5194-20 -chr17 41209154 41209172 BRCA1(NM_0072943):c5277+20 -chr17 41215329 41215347 BRCA1(NM_0072943):c5153-20 -chr17 41215392 41215410 BRCA1(NM_0072943):c5193+20 -chr17 41215870 41215888 BRCA1(NM_0072943):c5075-20 -chr17 41215970 41215988 BRCA1(NM_0072943):c5152+20 -chr17 41219604 41219622 BRCA1(NM_0072943):c4987-20 -chr17 41219714 41219732 BRCA1(NM_0072943):c5074+20 -chr17 41222924 41222942 BRCA1(NM_0072943):c4676-20 -chr17 41223257 41223275 BRCA1(NM_0072943):c4986+20 -chr17 41226327 41226345 BRCA1(NM_0072943):c4485-20 -chr17 41226540 41226558 BRCA1(NM_0072943):c4675+20 -chr17 41228484 41228502 BRCA1(NM_0072943):c4358-20 -chr17 41228633 41228651 BRCA1(NM_0072943):c4484+20 -chr17 41234400 41234418 BRCA1(NM_0072943):c4186-20 -chr17 41234594 41234612 BRCA1(NM_0072943):c4357+20 -chr17 41242940 41242958 BRCA1(NM_0072943):c4097-20 -chr17 41243051 41243069 BRCA1(NM_0072943):c4185+20 -chr17 41243431 41243449 BRCA1(NM_0072943):c671-20 -chr17 41246879 41246897 BRCA1(NM_0072943):c4096+20 -chr17 41247842 41247860 BRCA1(NM_0072943):c594-20 -chr17 41247941 41247959 BRCA1(NM_0072943):c670+20 -chr17 41249240 41249258 BRCA1(NM_0072943):c548-20 -chr17 41249308 41249326 BRCA1(NM_0072943):c593+20 -chr17 41251771 41251789 BRCA1(NM_0072943):c442-20 -chr17 41251899 41251917 BRCA1(NM_0072943):c547+20 -chr17 41256118 41256136 BRCA1(NM_0072943):c302-20 -chr17 41256280 41256298 BRCA1(NM_0072943):c441+20 -chr17 41256864 41256882 BRCA1(NM_0072943):c213-20 -chr17 41256975 41256993 BRCA1(NM_0072943):c301+20 -chr17 41258452 41258470 BRCA1(NM_0072943):c135-20 -chr17 41258552 41258570 BRCA1(NM_0072943):c212+20 -chr17 41267722 41267740 BRCA1(NM_0072943):c81-20 -chr17 41267798 41267816 BRCA1(NM_0072943):c134+20 -chr17 41276013 41276031 BRCA1(NM_0072943):c1-20 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ATRX(NM_0004893):c6326+5 -chrX 76845298 76845301 ATRX(NM_0004893):c6111-5 -chrX 76845412 76845415 ATRX(NM_0004893):c6217+5 -chrX 76849160 76849163 ATRX(NM_0004893):c5957-5 -chrX 76849321 76849324 ATRX(NM_0004893):c6110+5 -chrX 76854874 76854877 ATRX(NM_0004893):c5787-5 -chrX 76855051 76855054 ATRX(NM_0004893):c5956+5 -chrX 76855195 76855198 ATRX(NM_0004893):c5698-5 -chrX 76855291 76855294 ATRX(NM_0004893):c5786+5 -chrX 76855897 76855900 ATRX(NM_0004893):c5567-5 -chrX 76856035 76856038 ATRX(NM_0004893):c5697+5 -chrX 76872075 76872078 ATRX(NM_0004893):c5449-5 -chrX 76872200 76872203 ATRX(NM_0004893):c5566+5 -chrX 76874268 76874271 ATRX(NM_0004893):c5273-5 -chrX 76874451 76874454 ATRX(NM_0004893):c5448+5 -chrX 76875857 76875860 ATRX(NM_0004893):c5135-5 -chrX 76876002 76876005 ATRX(NM_0004893):c5272+5 -chrX 76888689 76888692 ATRX(NM_0004893):c4957-5 -chrX 76888874 76888877 ATRX(NM_0004893):c5134+5 -chrX 76889048 76889051 ATRX(NM_0004893):c4810-5 -chrX 76889202 76889205 ATRX(NM_0004893):c4956+5 -chrX 76890079 76890082 ATRX(NM_0004893):c4700-5 -chrX 76890196 76890199 ATRX(NM_0004893):c4809+5 -chrX 76891400 76891403 ATRX(NM_0004893):c4558-5 -chrX 76891549 76891552 ATRX(NM_0004893):c4699+5 -chrX 76907598 76907601 ATRX(NM_0004893):c4318-5 -chrX 76907845 76907848 ATRX(NM_0004893):c4557+5 -chrX 76909582 76909585 ATRX(NM_0004893):c4215-5 -chrX 76909692 76909695 ATRX(NM_0004893):c4317+5 -chrX 76912044 76912047 ATRX(NM_0004893):c4121-5 -chrX 76912145 76912148 ATRX(NM_0004893):c4214+5 -chrX 76918865 76918868 ATRX(NM_0004893):c3944-5 -chrX 76919049 76919052 ATRX(NM_0004893):c4120+5 -chrX 76920128 76920131 ATRX(NM_0004893):c3810-5 -chrX 76920269 76920272 ATRX(NM_0004893):c3943+5 -chrX 76931715 76931718 ATRX(NM_0004893):c3737-5 -chrX 76931795 76931798 ATRX(NM_0004893):c3809+5 -chrX 76937006 76937009 ATRX(NM_0004893):c663-5 -chrX 76940087 76940090 ATRX(NM_0004893):c3736+5 -chrX 76940425 76940428 ATRX(NM_0004893):c595-5 -chrX 76940500 76940503 ATRX(NM_0004893):c662+5 -chrX 76944305 76944308 ATRX(NM_0004893):c485-5 -chrX 76944422 76944425 ATRX(NM_0004893):c594+5 -chrX 76949307 76949310 ATRX(NM_0004893):c371-5 -chrX 76949428 76949431 ATRX(NM_0004893):c484+5 -chrX 76952059 76952062 ATRX(NM_0004893):c243-5 -chrX 76952194 76952197 ATRX(NM_0004893):c370+5 -chrX 76953065 76953068 ATRX(NM_0004893):c190-5 -chrX 76953125 76953128 ATRX(NM_0004893):c242+5 -chrX 76954056 76954059 ATRX(NM_0004893):c134-5 -chrX 76954119 76954122 ATRX(NM_0004893):c189+5 -chrX 76972602 76972605 ATRX(NM_0004893):c21-5 -chrX 76972722 76972725 ATRX(NM_0004893):c133+5 -chrX 77041462 77041465 ATRX(NM_0004893):c-5 -chrX 77041489 77041492 ATRX(NM_0004893):c20+5 diff --git a/hotspot_coverage/Colorectal_combined.bed b/hotspot_coverage/Colorectal_combined.bed deleted file mode 100644 index 8cdb69e..0000000 --- a/hotspot_coverage/Colorectal_combined.bed +++ /dev/null @@ -1,38 +0,0 @@ -chr1 115252201 115252204 NRAS(NM_002524.3):c.436_438 -chr1 115252288 115252291 NRAS(NM_002524.3):c.349_351 -chr1 115256527 115256530 NRAS(NM_002524.3):c.181_183 -chr1 115256533 115256536 NRAS(NM_002524.3):c.175_177 -chr1 115258742 115258748 NRAS(NM_002524.3):c.34_39 -chr3 178935992 178936127 PIK3CA(NM_006218.2):c.1540-5_1664+5 -chr3 178951876 178952157 PIK3CA(NM_006218.2):c.2937-5_*5 -chr7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -chr7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -chr7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -chr7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -chr7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 -chr12 25378559 25378562 KRAS(NM_004985.3):c.436_438 -chr12 25378646 25378649 KRAS(NM_004985.3):c.349_351 -chr12 25380274 25380277 KRAS(NM_004985.3):c.181_183 -chr12 25380280 25380283 KRAS(NM_004985.3):c.175_177 -chr12 25398279 25398285 KRAS(NM_004985.3):c.34_39 -chr10 89624221 89624310 PTEN(NM_000314.4):c.-6_79+5 -chr10 89653776 89653871 PTEN(NM_000314.4):c.80-5_164+5 -chr10 89685264 89685319 PTEN(NM_000314.4):c.165-5_209+5 -chr10 89690797 89690851 PTEN(NM_000314.4):c.210-5_253+5 -chr10 89692764 89693013 PTEN(NM_000314.4):c.254-5_492+5 -chr10 89711869 89712021 PTEN(NM_000314.4):c.493-5_634+5 -chr10 89717604 89717781 PTEN(NM_000314.4):c.635-5_801+5 -chr10 89720645 89720880 PTEN(NM_000314.4):c.802-5_1026+5 -chr10 89725038 89725234 PTEN(NM_000314.4):c.1027-5_*5 -chr17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T -chr17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5 -chr17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5 -chr17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5 -chr17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5 -chr17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5 -chr17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5 -chr17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5 -chr17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5 -chr17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5 -chr17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5 diff --git a/hotspot_coverage/Colorectal_combined.groups b/hotspot_coverage/Colorectal_combined.groups deleted file mode 100644 index 206972f..0000000 --- a/hotspot_coverage/Colorectal_combined.groups +++ /dev/null @@ -1,39 +0,0 @@ -GENE -NRAS -NRAS -NRAS -NRAS -NRAS -PIK3CA -PIK3CA -EGFR -EGFR -EGFR -EGFR -BRAF -BRAF -KRAS -KRAS -KRAS -KRAS -KRAS -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 diff --git a/hotspot_coverage/Colorectal_genescreen.bed b/hotspot_coverage/Colorectal_genescreen.bed deleted file mode 100644 index 143ba51..0000000 --- a/hotspot_coverage/Colorectal_genescreen.bed +++ /dev/null @@ -1,20 +0,0 @@ -chr10 89624221 89624310 PTEN(NM_000314.4):c.-6_79+5 -chr10 89653776 89653871 PTEN(NM_000314.4):c.80-5_164+5 -chr10 89685264 89685319 PTEN(NM_000314.4):c.165-5_209+5 -chr10 89690797 89690851 PTEN(NM_000314.4):c.210-5_253+5 -chr10 89692764 89693013 PTEN(NM_000314.4):c.254-5_492+5 -chr10 89711869 89712021 PTEN(NM_000314.4):c.493-5_634+5 -chr10 89717604 89717781 PTEN(NM_000314.4):c.635-5_801+5 -chr10 89720645 89720880 PTEN(NM_000314.4):c.802-5_1026+5 -chr10 89725038 89725234 PTEN(NM_000314.4):c.1027-5_*5 -chr17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T -chr17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5 -chr17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5 -chr17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5 -chr17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5 -chr17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5 -chr17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5 -chr17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5 -chr17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5 -chr17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5 -chr17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5 diff --git a/hotspot_coverage/Colorectal_genescreen.groups b/hotspot_coverage/Colorectal_genescreen.groups deleted file mode 100644 index 1415e15..0000000 --- a/hotspot_coverage/Colorectal_genescreen.groups +++ /dev/null @@ -1,21 +0,0 @@ -GENE -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 diff --git a/hotspot_coverage/Colorectal_hotspots.bed b/hotspot_coverage/Colorectal_hotspots.bed deleted file mode 100644 index 99fe979..0000000 --- a/hotspot_coverage/Colorectal_hotspots.bed +++ /dev/null @@ -1,18 +0,0 @@ -chr1 115252201 115252204 NRAS(NM_002524.3):c.436_438 -chr1 115252288 115252291 NRAS(NM_002524.3):c.349_351 -chr1 115256527 115256530 NRAS(NM_002524.3):c.181_183 -chr1 115256533 115256536 NRAS(NM_002524.3):c.175_177 -chr1 115258742 115258748 NRAS(NM_002524.3):c.34_39 -chr3 178935992 178936127 PIK3CA(NM_006218.2):c.1540-5_1664+5 -chr3 178951876 178952157 PIK3CA(NM_006218.2):c.2937-5_*5 -chr7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -chr7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -chr7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -chr7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -chr7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 -chr12 25378559 25378562 KRAS(NM_004985.3):c.436_438 -chr12 25378646 25378649 KRAS(NM_004985.3):c.349_351 -chr12 25380274 25380277 KRAS(NM_004985.3):c.181_183 -chr12 25380280 25380283 KRAS(NM_004985.3):c.175_177 -chr12 25398279 25398285 KRAS(NM_004985.3):c.34_39 diff --git a/hotspot_coverage/Colorectal_hotspots.groups b/hotspot_coverage/Colorectal_hotspots.groups deleted file mode 100644 index ba8d88f..0000000 --- a/hotspot_coverage/Colorectal_hotspots.groups +++ /dev/null @@ -1,19 +0,0 @@ -GENE -NRAS -NRAS -NRAS -NRAS -NRAS -PIK3CA -PIK3CA -EGFR -EGFR -EGFR -EGFR -BRAF -BRAF -KRAS -KRAS -KRAS -KRAS -KRAS diff --git a/hotspot_coverage/GIST_combined.bed b/hotspot_coverage/GIST_combined.bed deleted file mode 100644 index 0917f81..0000000 --- a/hotspot_coverage/GIST_combined.bed +++ /dev/null @@ -1,8 +0,0 @@ -chr4 55141002 55141145 PDGFRA(NM_006206.4):c.1654-5_1786+5 -chr4 55144057 55144178 PDGFRA(NM_006206.4):c.1892-5_2002+5 -chr4 55152002 55152135 PDGFRA(NM_006206.4):c.2440-5_2562+5 -chr4 55592017 55592221 KIT(NM_000222.2):c.1347-5_1540+5 -chr4 55593576 55593713 KIT(NM_000222.2):c.1648-5_1774+5 -chr4 55594171 55594292 KIT(NM_000222.2):c.1880-5_1990+5 -chr4 55595495 55595656 KIT(NM_000222.2):c.1991-5_2141+5 -chr4 55599230 55599363 KIT(NM_000222.2):c.2362-5_2484+5 diff --git a/hotspot_coverage/GIST_combined.groups b/hotspot_coverage/GIST_combined.groups deleted file mode 100644 index 3183fda..0000000 --- a/hotspot_coverage/GIST_combined.groups +++ /dev/null @@ -1,9 +0,0 @@ -GENE -PDGFRA -PDGFRA -PDGFRA -KIT -KIT -KIT -KIT -KIT diff --git a/hotspot_coverage/GIST_hotspots.bed b/hotspot_coverage/GIST_hotspots.bed deleted file mode 100644 index 0917f81..0000000 --- a/hotspot_coverage/GIST_hotspots.bed +++ /dev/null @@ -1,8 +0,0 @@ -chr4 55141002 55141145 PDGFRA(NM_006206.4):c.1654-5_1786+5 -chr4 55144057 55144178 PDGFRA(NM_006206.4):c.1892-5_2002+5 -chr4 55152002 55152135 PDGFRA(NM_006206.4):c.2440-5_2562+5 -chr4 55592017 55592221 KIT(NM_000222.2):c.1347-5_1540+5 -chr4 55593576 55593713 KIT(NM_000222.2):c.1648-5_1774+5 -chr4 55594171 55594292 KIT(NM_000222.2):c.1880-5_1990+5 -chr4 55595495 55595656 KIT(NM_000222.2):c.1991-5_2141+5 -chr4 55599230 55599363 KIT(NM_000222.2):c.2362-5_2484+5 diff --git a/hotspot_coverage/GIST_hotspots.groups b/hotspot_coverage/GIST_hotspots.groups deleted file mode 100644 index 3183fda..0000000 --- a/hotspot_coverage/GIST_hotspots.groups +++ /dev/null @@ -1,9 +0,0 @@ -GENE -PDGFRA -PDGFRA -PDGFRA -KIT -KIT -KIT -KIT -KIT diff --git a/hotspot_coverage/Glioma_combined.bed b/hotspot_coverage/Glioma_combined.bed deleted file mode 100644 index f5c570c..0000000 --- a/hotspot_coverage/Glioma_combined.bed +++ /dev/null @@ -1,69 +0,0 @@ -chr1 226252133 226252136 H3F3A(NM_002107.4):c.82_84 -chr1 226252154 226252157 H3F3A(NM_002107.4):c.103_105 -chr2 209113110 209113113 IDH1(NM_005896.2):c.394_396 -chr5 1295227 1295228 TERT(NM_198253.2):c.-124_-124 -chr5 1295249 1295250 TERT(NM_198253.2):c.-146_-146 -chr7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -chr7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -chr7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -chr7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -chr15 90631836 90631839 IDH2(NM_002168.2):c.514_516 -chr9 21974671 21974831 CDKN2A(NM_000077.3):c.150+5_-5 -chr9 21970895 21971212 CDKN2A(NM_000077.3):c.151-5_457+5 -chr9 21968222 21968246 CDKN2A(NM_000077.3):c.*6_458-5 -chr10 89624221 89624310 PTEN(NM_000314.4):c.-6_79+5 -chr10 89653776 89653871 PTEN(NM_000314.4):c.80-5_164+5 -chr10 89685264 89685319 PTEN(NM_000314.4):c.165-5_209+5 -chr10 89690797 89690851 PTEN(NM_000314.4):c.210-5_253+5 -chr10 89692764 89693013 PTEN(NM_000314.4):c.254-5_492+5 -chr10 89711869 89712021 PTEN(NM_000314.4):c.493-5_634+5 -chr10 89717604 89717781 PTEN(NM_000314.4):c.635-5_801+5 -chr10 89720645 89720880 PTEN(NM_000314.4):c.802-5_1026+5 -chr10 89725038 89725234 PTEN(NM_000314.4):c.1027-5_*5 -chr17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T -chr17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5 -chr17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5 -chr17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5 -chr17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5 -chr17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5 -chr17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5 -chr17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5 -chr17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5 -chr17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5 -chr17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5 -chrX 76763824 76764113 ATRX(NM_000489.3):c.7201-6_c*5 -chrX 76776260 76776399 ATRX(NM_000489.3):c.7072-5_7200+5 -chrX 76776875 76776981 ATRX(NM_000489.3):c.6976-5_7071+5 -chrX 76777735 76777871 ATRX(NM_000489.3):c.6850-5_6975+5 -chrX 76778724 76778884 ATRX(NM_000489.3):c.6700-5_6849+5 -chrX 76812916 76813121 ATRX(NM_000489.3):c.6505-5_6699+5 -chrX 76814134 76814322 ATRX(NM_000489.3):c.6327-5_6504+5 -chrX 76829709 76829828 ATRX(NM_000489.3):c.6218-5_6326+5 -chrX 76845298 76845415 ATRX(NM_000489.3):c.6111-5_6217+5 -chrX 76849160 76849324 ATRX(NM_000489.3):c.5957-5_6110+5 -chrX 76854874 76855054 ATRX(NM_000489.3):c.5787-5_5956+5 -chrX 76855195 76855294 ATRX(NM_000489.3):c.5698-5_5786+5 -chrX 76855897 76856038 ATRX(NM_000489.3):c.5567-5_5697+5 -chrX 76872075 76872203 ATRX(NM_000489.3):c.5449-5_5566+5 -chrX 76874268 76874454 ATRX(NM_000489.3):c.5273-5_5448+5 -chrX 76875857 76876005 ATRX(NM_000489.3):c.5135-5_5272+5 -chrX 76888689 76888877 ATRX(NM_000489.3):c.4957-5_5134+5 -chrX 76889048 76889205 ATRX(NM_000489.3):c.4810-5_4956+5 -chrX 76890079 76890199 ATRX(NM_000489.3):c.4700-5_4809+5 -chrX 76891400 76891552 ATRX(NM_000489.3):c.4558-5_4699+5 -chrX 76907598 76907848 ATRX(NM_000489.3):c.4318-5_4557+5 -chrX 76909582 76909695 ATRX(NM_000489.3):c.4215-5_4317+5 -chrX 76912044 76912148 ATRX(NM_000489.3):c.4121-5_4214+5 -chrX 76918865 76919052 ATRX(NM_000489.3):c.3944-5_4120+5 -chrX 76920128 76920272 ATRX(NM_000489.3):c.3810-5_3943+5 -chrX 76931715 76931798 ATRX(NM_000489.3):c.3737-5_3809+5 -chrX 76937006 76940090 ATRX(NM_000489.3):c.663-5_3736+5 -chrX 76940425 76940503 ATRX(NM_000489.3):c.595-5_662+5 -chrX 76944305 76944425 ATRX(NM_000489.3):c.485-5_594+5 -chrX 76949307 76949431 ATRX(NM_000489.3):c.371-5_484+5 -chrX 76952059 76952197 ATRX(NM_000489.3):c.243-5_370+5 -chrX 76953065 76953128 ATRX(NM_000489.3):c.190-5_242+5 -chrX 76954056 76954122 ATRX(NM_000489.3):c.134-5_189+5 -chrX 76972602 76972725 ATRX(NM_000489.3):c.21-5_133+5 -chrX 77041462 77041492 ATRX(NM_000489.3):c.-5_20+5 diff --git a/hotspot_coverage/Glioma_combined.groups b/hotspot_coverage/Glioma_combined.groups deleted file mode 100644 index fc94f6a..0000000 --- a/hotspot_coverage/Glioma_combined.groups +++ /dev/null @@ -1,70 +0,0 @@ -GENE -H3F3A -H3F3A -IDH1 -TERT -TERT -EGFR -EGFR -EGFR -EGFR -BRAF -IDH2 -CDKN2A -CDKN2A -CDKN2A -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX diff --git a/hotspot_coverage/Glioma_genescreen.bed b/hotspot_coverage/Glioma_genescreen.bed deleted file mode 100644 index 502ead4..0000000 --- a/hotspot_coverage/Glioma_genescreen.bed +++ /dev/null @@ -1,58 +0,0 @@ -chr9 21974671 21974831 CDKN2A(NM_000077.3):c.150+5_-5 -chr9 21970895 21971212 CDKN2A(NM_000077.3):c.151-5_457+5 -chr9 21968222 21968246 CDKN2A(NM_000077.3):c.*6_458-5 -chr10 89624221 89624310 PTEN(NM_000314.4):c.-6_79+5 -chr10 89653776 89653871 PTEN(NM_000314.4):c.80-5_164+5 -chr10 89685264 89685319 PTEN(NM_000314.4):c.165-5_209+5 -chr10 89690797 89690851 PTEN(NM_000314.4):c.210-5_253+5 -chr10 89692764 89693013 PTEN(NM_000314.4):c.254-5_492+5 -chr10 89711869 89712021 PTEN(NM_000314.4):c.493-5_634+5 -chr10 89717604 89717781 PTEN(NM_000314.4):c.635-5_801+5 -chr10 89720645 89720880 PTEN(NM_000314.4):c.802-5_1026+5 -chr10 89725038 89725234 PTEN(NM_000314.4):c.1027-5_*5 -chr17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T -chr17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5 -chr17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5 -chr17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5 -chr17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5 -chr17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5 -chr17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5 -chr17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5 -chr17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5 -chr17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5 -chr17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5 -chrX 76763824 76764113 ATRX(NM_000489.3):c.7201-6_c*5 -chrX 76776260 76776399 ATRX(NM_000489.3):c.7072-5_7200+5 -chrX 76776875 76776981 ATRX(NM_000489.3):c.6976-5_7071+5 -chrX 76777735 76777871 ATRX(NM_000489.3):c.6850-5_6975+5 -chrX 76778724 76778884 ATRX(NM_000489.3):c.6700-5_6849+5 -chrX 76812916 76813121 ATRX(NM_000489.3):c.6505-5_6699+5 -chrX 76814134 76814322 ATRX(NM_000489.3):c.6327-5_6504+5 -chrX 76829709 76829828 ATRX(NM_000489.3):c.6218-5_6326+5 -chrX 76845298 76845415 ATRX(NM_000489.3):c.6111-5_6217+5 -chrX 76849160 76849324 ATRX(NM_000489.3):c.5957-5_6110+5 -chrX 76854874 76855054 ATRX(NM_000489.3):c.5787-5_5956+5 -chrX 76855195 76855294 ATRX(NM_000489.3):c.5698-5_5786+5 -chrX 76855897 76856038 ATRX(NM_000489.3):c.5567-5_5697+5 -chrX 76872075 76872203 ATRX(NM_000489.3):c.5449-5_5566+5 -chrX 76874268 76874454 ATRX(NM_000489.3):c.5273-5_5448+5 -chrX 76875857 76876005 ATRX(NM_000489.3):c.5135-5_5272+5 -chrX 76888689 76888877 ATRX(NM_000489.3):c.4957-5_5134+5 -chrX 76889048 76889205 ATRX(NM_000489.3):c.4810-5_4956+5 -chrX 76890079 76890199 ATRX(NM_000489.3):c.4700-5_4809+5 -chrX 76891400 76891552 ATRX(NM_000489.3):c.4558-5_4699+5 -chrX 76907598 76907848 ATRX(NM_000489.3):c.4318-5_4557+5 -chrX 76909582 76909695 ATRX(NM_000489.3):c.4215-5_4317+5 -chrX 76912044 76912148 ATRX(NM_000489.3):c.4121-5_4214+5 -chrX 76918865 76919052 ATRX(NM_000489.3):c.3944-5_4120+5 -chrX 76920128 76920272 ATRX(NM_000489.3):c.3810-5_3943+5 -chrX 76931715 76931798 ATRX(NM_000489.3):c.3737-5_3809+5 -chrX 76937006 76940090 ATRX(NM_000489.3):c.663-5_3736+5 -chrX 76940425 76940503 ATRX(NM_000489.3):c.595-5_662+5 -chrX 76944305 76944425 ATRX(NM_000489.3):c.485-5_594+5 -chrX 76949307 76949431 ATRX(NM_000489.3):c.371-5_484+5 -chrX 76952059 76952197 ATRX(NM_000489.3):c.243-5_370+5 -chrX 76953065 76953128 ATRX(NM_000489.3):c.190-5_242+5 -chrX 76954056 76954122 ATRX(NM_000489.3):c.134-5_189+5 -chrX 76972602 76972725 ATRX(NM_000489.3):c.21-5_133+5 -chrX 77041462 77041492 ATRX(NM_000489.3):c.-5_20+5 diff --git a/hotspot_coverage/Glioma_genescreen.groups b/hotspot_coverage/Glioma_genescreen.groups deleted file mode 100644 index 60e5715..0000000 --- a/hotspot_coverage/Glioma_genescreen.groups +++ /dev/null @@ -1,59 +0,0 @@ -GENE -CDKN2A -CDKN2A -CDKN2A -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX diff --git a/hotspot_coverage/Glioma_hotspots.bed b/hotspot_coverage/Glioma_hotspots.bed deleted file mode 100644 index d418cff..0000000 --- a/hotspot_coverage/Glioma_hotspots.bed +++ /dev/null @@ -1,11 +0,0 @@ -chr1 226252133 226252136 H3F3A(NM_002107.4):c.82_84 -chr1 226252154 226252157 H3F3A(NM_002107.4):c.103_105 -chr2 209113110 209113113 IDH1(NM_005896.2):c.394_396 -chr5 1295227 1295228 TERT(NM_198253.2):c.-124_-124 -chr5 1295249 1295250 TERT(NM_198253.2):c.-146_-146 -chr7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -chr7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -chr7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -chr7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -chr15 90631836 90631839 IDH2(NM_002168.2):c.514_516 diff --git a/hotspot_coverage/Glioma_hotspots.groups b/hotspot_coverage/Glioma_hotspots.groups deleted file mode 100644 index 76fd6d4..0000000 --- a/hotspot_coverage/Glioma_hotspots.groups +++ /dev/null @@ -1,12 +0,0 @@ -GENE -H3F3A -H3F3A -IDH1 -TERT -TERT -EGFR -EGFR -EGFR -EGFR -BRAF -IDH2 diff --git a/hotspot_coverage/Lung_combined.bed b/hotspot_coverage/Lung_combined.bed deleted file mode 100644 index 7697037..0000000 --- a/hotspot_coverage/Lung_combined.bed +++ /dev/null @@ -1,11 +0,0 @@ -chr7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -chr7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -chr7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -chr7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -chr7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 -chr12 25378559 25378562 KRAS(NM_004985.3):c.436_438 -chr12 25378646 25378649 KRAS(NM_004985.3):c.349_351 -chr12 25380274 25380277 KRAS(NM_004985.3):c.181_183 -chr12 25380280 25380283 KRAS(NM_004985.3):c.175_177 -chr12 25398279 25398285 KRAS(NM_004985.3):c.34_39 diff --git a/hotspot_coverage/Lung_combined.groups b/hotspot_coverage/Lung_combined.groups deleted file mode 100644 index 9b60718..0000000 --- a/hotspot_coverage/Lung_combined.groups +++ /dev/null @@ -1,12 +0,0 @@ -GENE -EGFR -EGFR -EGFR -EGFR -BRAF -BRAF -KRAS -KRAS -KRAS -KRAS -KRAS diff --git a/hotspot_coverage/Lung_hotspots.bed b/hotspot_coverage/Lung_hotspots.bed deleted file mode 100644 index 7697037..0000000 --- a/hotspot_coverage/Lung_hotspots.bed +++ /dev/null @@ -1,11 +0,0 @@ -chr7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -chr7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -chr7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -chr7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -chr7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 -chr12 25378559 25378562 KRAS(NM_004985.3):c.436_438 -chr12 25378646 25378649 KRAS(NM_004985.3):c.349_351 -chr12 25380274 25380277 KRAS(NM_004985.3):c.181_183 -chr12 25380280 25380283 KRAS(NM_004985.3):c.175_177 -chr12 25398279 25398285 KRAS(NM_004985.3):c.34_39 diff --git a/hotspot_coverage/Lung_hotspots.groups b/hotspot_coverage/Lung_hotspots.groups deleted file mode 100644 index 9b60718..0000000 --- a/hotspot_coverage/Lung_hotspots.groups +++ /dev/null @@ -1,12 +0,0 @@ -GENE -EGFR -EGFR -EGFR -EGFR -BRAF -BRAF -KRAS -KRAS -KRAS -KRAS -KRAS diff --git a/hotspot_coverage/Melanoma_combined.bed b/hotspot_coverage/Melanoma_combined.bed deleted file mode 100644 index 7ab0ed8..0000000 --- a/hotspot_coverage/Melanoma_combined.bed +++ /dev/null @@ -1,12 +0,0 @@ -chr1 115252201 115252204 NRAS(NM_002524.3):c.436_438 -chr1 115252288 115252291 NRAS(NM_002524.3):c.349_351 -chr1 115256527 115256530 NRAS(NM_002524.3):c.181_183 -chr1 115256533 115256536 NRAS(NM_002524.3):c.175_177 -chr1 115258742 115258748 NRAS(NM_002524.3):c.34_39 -chr4 55592017 55592221 KIT(NM_000222.2):c.1347-5_1540+5 -chr4 55593576 55593713 KIT(NM_000222.2):c.1648-5_1774+5 -chr4 55594171 55594292 KIT(NM_000222.2):c.1880-5_1990+5 -chr4 55595495 55595656 KIT(NM_000222.2):c.1991-5_2141+5 -chr4 55599230 55599363 KIT(NM_000222.2):c.2362-5_2484+5 -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -chr7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 diff --git a/hotspot_coverage/Melanoma_combined.groups b/hotspot_coverage/Melanoma_combined.groups deleted file mode 100644 index 77c5e61..0000000 --- a/hotspot_coverage/Melanoma_combined.groups +++ /dev/null @@ -1,13 +0,0 @@ -GENE -NRAS -NRAS -NRAS -NRAS -NRAS -KIT -KIT -KIT -KIT -KIT -BRAF -BRAF diff --git a/hotspot_coverage/Melanoma_hotspots.bed b/hotspot_coverage/Melanoma_hotspots.bed deleted file mode 100644 index 7ab0ed8..0000000 --- a/hotspot_coverage/Melanoma_hotspots.bed +++ /dev/null @@ -1,12 +0,0 @@ -chr1 115252201 115252204 NRAS(NM_002524.3):c.436_438 -chr1 115252288 115252291 NRAS(NM_002524.3):c.349_351 -chr1 115256527 115256530 NRAS(NM_002524.3):c.181_183 -chr1 115256533 115256536 NRAS(NM_002524.3):c.175_177 -chr1 115258742 115258748 NRAS(NM_002524.3):c.34_39 -chr4 55592017 55592221 KIT(NM_000222.2):c.1347-5_1540+5 -chr4 55593576 55593713 KIT(NM_000222.2):c.1648-5_1774+5 -chr4 55594171 55594292 KIT(NM_000222.2):c.1880-5_1990+5 -chr4 55595495 55595656 KIT(NM_000222.2):c.1991-5_2141+5 -chr4 55599230 55599363 KIT(NM_000222.2):c.2362-5_2484+5 -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -chr7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 diff --git a/hotspot_coverage/Melanoma_hotspots.groups b/hotspot_coverage/Melanoma_hotspots.groups deleted file mode 100644 index 77c5e61..0000000 --- a/hotspot_coverage/Melanoma_hotspots.groups +++ /dev/null @@ -1,13 +0,0 @@ -GENE -NRAS -NRAS -NRAS -NRAS -NRAS -KIT -KIT -KIT -KIT -KIT -BRAF -BRAF diff --git a/hotspot_coverage/Thyroid_combined.bed b/hotspot_coverage/Thyroid_combined.bed deleted file mode 100644 index 6e6bfb1..0000000 --- a/hotspot_coverage/Thyroid_combined.bed +++ /dev/null @@ -1,44 +0,0 @@ -chr1 115252201 115252204 NRAS(NM_002524.3):c.436_438(exon4_A146) -chr1 115252288 115252291 NRAS(NM_002524.3):c.349_351(exon4_K117) -chr1 115256527 115256530 NRAS(NM_002524.3):c.181_183(exon3_Q61) -chr1 115256533 115256536 NRAS(NM_002524.3):c.175_177(exon3_A59) -chr1 115258742 115258748 NRAS(NM_002524.3):c.34_39(exon2_G12-G13) -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5(exon15) -chr10 43572701 43572784 RET(NM_020975.4):c.-5_73+5(exon1) -chr10 43595901 43596175 RET(NM_020975.4):c.74-5_337+5(exon2) -chr10 43597784 43598082 RET(NM_020975.4):c.338-5_625+5(exon3) -chr10 43600394 43600646 RET(NM_020975.4):c.626-5_867+5(exon4) -chr10 43601818 43602024 RET(NM_020975.4):c.868-5_1063+5(exon5) -chr10 43604473 43604683 RET(NM_020975.4):c.1064-5_1263+5(exon6) -chr10 43606649 43606918 RET(NM_020975.4):c.1264-5_1522+5(exon7) -chr10 43607541 43607677 RET(NM_020975.4):c.1523-5_1648+5(exon8) -chr10 43608295 43608416 RET(NM_020975.4):c.1649-5_1759+5(exon9) -chr10 43608998 43609128 RET(NM_020975.4):c.1760-5_1879+5(exon10) -chr10 43609922 43610189 RET(NM_020975.4):c.1880-5_2136+5(exon11) -chr10 43612026 43612184 RET(NM_020975.4):c.2137-5_2284+5(exon12) -chr10 43613815 43613933 RET(NM_020975.4):c.2285-5_2392+5(exon13) -chr10 43614973 43615198 RET(NM_020975.4):c.2393-5_2607+5(exon14) -chr10 43615523 43615656 RET(NM_020975.4):c.2608-5_2730+5(exon15) -chr10 43617388 43617469 RET(NM_020975.4):c.2731-5_2801+5(exon16) -chr10 43619113 43619261 RET(NM_020975.4):c.2802-5_2939+5(exon17) -chr10 43620325 43620435 RET(NM_020975.4):c.2940-5_3039+5(exon18) -chr10 43622017 43622175 RET(NM_020975.4):c.3040-5_3187+5(exon19) -chr10 43623554 43623722 RET(NM_020975.4):c.3188-5_*5(exon20) -chr11 533872 533875 HRAS(NM_005343.2):c.181_183(exon3_Q61) -chr11 534283 534289 HRAS(NM_005343.2):c.34_39(exon2_G12-G13) -chr12 25378559 25378562 KRAS(NM_004985.3):c.436_438(exon4_A146) -chr12 25378646 25378649 KRAS(NM_004985.3):c.349_351(exon4_K117) -chr12 25380274 25380277 KRAS(NM_004985.3):c.181_183(exon3_Q61) -chr12 25380280 25380283 KRAS(NM_004985.3):c.175_177(exon3_A59) -chr12 25398279 25398285 KRAS(NM_004985.3):c.34_39(exon2_G12-G13) -chr17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5(exon11) -chr17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5(exon10) -chr17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T(exon10alt) -chr17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5(exon9) -chr17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5(exon8) -chr17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5(exon7) -chr17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5(exon6) -chr17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5(exon5) -chr17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5(exon4) -chr17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5(exon3) -chr17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5(exon2) diff --git a/hotspot_coverage/Thyroid_combined.groups b/hotspot_coverage/Thyroid_combined.groups deleted file mode 100644 index f3a9642..0000000 --- a/hotspot_coverage/Thyroid_combined.groups +++ /dev/null @@ -1,45 +0,0 @@ -GENE -NRAS -NRAS -NRAS -NRAS -NRAS -BRAF -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -HRAS -HRAS -KRAS -KRAS -KRAS -KRAS -KRAS -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 diff --git a/hotspot_coverage/Thyroid_genescreen.bed b/hotspot_coverage/Thyroid_genescreen.bed deleted file mode 100644 index ad01253..0000000 --- a/hotspot_coverage/Thyroid_genescreen.bed +++ /dev/null @@ -1,31 +0,0 @@ -chr10 43572701 43572784 RET(NM_020975.4):c.-5_73+5(exon1) -chr10 43595901 43596175 RET(NM_020975.4):c.74-5_337+5(exon2) -chr10 43597784 43598082 RET(NM_020975.4):c.338-5_625+5(exon3) -chr10 43600394 43600646 RET(NM_020975.4):c.626-5_867+5(exon4) -chr10 43601818 43602024 RET(NM_020975.4):c.868-5_1063+5(exon5) -chr10 43604473 43604683 RET(NM_020975.4):c.1064-5_1263+5(exon6) -chr10 43606649 43606918 RET(NM_020975.4):c.1264-5_1522+5(exon7) -chr10 43607541 43607677 RET(NM_020975.4):c.1523-5_1648+5(exon8) -chr10 43608295 43608416 RET(NM_020975.4):c.1649-5_1759+5(exon9) -chr10 43608998 43609128 RET(NM_020975.4):c.1760-5_1879+5(exon10) -chr10 43609922 43610189 RET(NM_020975.4):c.1880-5_2136+5(exon11) -chr10 43612026 43612184 RET(NM_020975.4):c.2137-5_2284+5(exon12) -chr10 43613815 43613933 RET(NM_020975.4):c.2285-5_2392+5(exon13) -chr10 43614973 43615198 RET(NM_020975.4):c.2393-5_2607+5(exon14) -chr10 43615523 43615656 RET(NM_020975.4):c.2608-5_2730+5(exon15) -chr10 43617388 43617469 RET(NM_020975.4):c.2731-5_2801+5(exon16) -chr10 43619113 43619261 RET(NM_020975.4):c.2802-5_2939+5(exon17) -chr10 43620325 43620435 RET(NM_020975.4):c.2940-5_3039+5(exon18) -chr10 43622017 43622175 RET(NM_020975.4):c.3040-5_3187+5(exon19) -chr10 43623554 43623722 RET(NM_020975.4):c.3188-5_*5(exon20) -chr17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5(exon11) -chr17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5(exon10) -chr17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T(exon10alt) -chr17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5(exon9) -chr17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5(exon8) -chr17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5(exon7) -chr17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5(exon6) -chr17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5(exon5) -chr17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5(exon4) -chr17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5(exon3) -chr17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5(exon2) diff --git a/hotspot_coverage/Thyroid_genescreen.groups b/hotspot_coverage/Thyroid_genescreen.groups deleted file mode 100644 index 63d6aea..0000000 --- a/hotspot_coverage/Thyroid_genescreen.groups +++ /dev/null @@ -1,32 +0,0 @@ -GENE -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -RET -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 diff --git a/hotspot_coverage/Thyroid_hotspots.bed b/hotspot_coverage/Thyroid_hotspots.bed deleted file mode 100644 index 4ef7414..0000000 --- a/hotspot_coverage/Thyroid_hotspots.bed +++ /dev/null @@ -1,13 +0,0 @@ -chr1 115252201 115252204 NRAS(NM_002524.3):c.436_438(exon4_A146) -chr1 115252288 115252291 NRAS(NM_002524.3):c.349_351(exon4_K117) -chr1 115256527 115256530 NRAS(NM_002524.3):c.181_183(exon3_Q61) -chr1 115256533 115256536 NRAS(NM_002524.3):c.175_177(exon3_A59) -chr1 115258742 115258748 NRAS(NM_002524.3):c.34_39(exon2_G12-G13) -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5(exon15) -chr11 533872 533875 HRAS(NM_005343.2):c.181_183(exon3_Q61) -chr11 534283 534289 HRAS(NM_005343.2):c.34_39(exon2_G12-G13) -chr12 25378559 25378562 KRAS(NM_004985.3):c.436_438(exon4_A146) -chr12 25378646 25378649 KRAS(NM_004985.3):c.349_351(exon4_K117) -chr12 25380274 25380277 KRAS(NM_004985.3):c.181_183(exon3_Q61) -chr12 25380280 25380283 KRAS(NM_004985.3):c.175_177(exon3_A59) -chr12 25398279 25398285 KRAS(NM_004985.3):c.34_39(exon2_G12-G13) diff --git a/hotspot_coverage/Thyroid_hotspots.groups b/hotspot_coverage/Thyroid_hotspots.groups deleted file mode 100644 index 2077f45..0000000 --- a/hotspot_coverage/Thyroid_hotspots.groups +++ /dev/null @@ -1,14 +0,0 @@ -GENE -NRAS -NRAS -NRAS -NRAS -NRAS -BRAF -HRAS -HRAS -KRAS -KRAS -KRAS -KRAS -KRAS diff --git a/hotspot_coverage/Tumour_combined.bed b/hotspot_coverage/Tumour_combined.bed deleted file mode 100644 index 4ee5a83..0000000 --- a/hotspot_coverage/Tumour_combined.bed +++ /dev/null @@ -1,185 +0,0 @@ -chrX 66764983 66766609 AR(NM_000044.2):c.-6_1616+5 -chrX 66863092 66863254 AR(NM_000044.2):c.1617-5_1768+5 -chrX 66905846 66905973 AR(NM_000044.2):c.1769-5_1885+5 -chrX 66931238 66931536 AR(NM_000044.2):c.1886-5_2173+5 -chrX 66937314 66937469 AR(NM_000044.2):c.2174-5_2318+5 -chrX 66941669 66941810 AR(NM_000044.2):c.2319-5_2449+5 -chrX 66942663 66942831 AR(NM_000044.2):c.2450-5_2607+5 -chrX 66943522 66943688 AR(NM_000044.2):c.2608-5_*5 -chrX 76763824 76764113 ATRX(NM_000489.3):c.7201-6_c*5 -chrX 76776260 76776399 ATRX(NM_000489.3):c.7072-5_7200+5 -chrX 76776875 76776981 ATRX(NM_000489.3):c.6976-5_7071+5 -chrX 76777735 76777871 ATRX(NM_000489.3):c.6850-5_6975+5 -chrX 76778724 76778884 ATRX(NM_000489.3):c.6700-5_6849+5 -chrX 76812916 76813121 ATRX(NM_000489.3):c.6505-5_6699+5 -chrX 76814134 76814322 ATRX(NM_000489.3):c.6327-5_6504+5 -chrX 76829709 76829828 ATRX(NM_000489.3):c.6218-5_6326+5 -chrX 76845298 76845415 ATRX(NM_000489.3):c.6111-5_6217+5 -chrX 76849160 76849324 ATRX(NM_000489.3):c.5957-5_6110+5 -chrX 76854874 76855054 ATRX(NM_000489.3):c.5787-5_5956+5 -chrX 76855195 76855294 ATRX(NM_000489.3):c.5698-5_5786+5 -chrX 76855897 76856038 ATRX(NM_000489.3):c.5567-5_5697+5 -chrX 76872075 76872203 ATRX(NM_000489.3):c.5449-5_5566+5 -chrX 76874268 76874454 ATRX(NM_000489.3):c.5273-5_5448+5 -chrX 76875857 76876005 ATRX(NM_000489.3):c.5135-5_5272+5 -chrX 76888689 76888877 ATRX(NM_000489.3):c.4957-5_5134+5 -chrX 76889048 76889205 ATRX(NM_000489.3):c.4810-5_4956+5 -chrX 76890079 76890199 ATRX(NM_000489.3):c.4700-5_4809+5 -chrX 76891400 76891552 ATRX(NM_000489.3):c.4558-5_4699+5 -chrX 76907598 76907848 ATRX(NM_000489.3):c.4318-5_4557+5 -chrX 76909582 76909695 ATRX(NM_000489.3):c.4215-5_4317+5 -chrX 76912044 76912148 ATRX(NM_000489.3):c.4121-5_4214+5 -chrX 76918865 76919052 ATRX(NM_000489.3):c.3944-5_4120+5 -chrX 76920128 76920272 ATRX(NM_000489.3):c.3810-5_3943+5 -chrX 76931715 76931798 ATRX(NM_000489.3):c.3737-5_3809+5 -chrX 76937006 76940090 ATRX(NM_000489.3):c.663-5_3736+5 -chrX 76940425 76940503 ATRX(NM_000489.3):c.595-5_662+5 -chrX 76944305 76944425 ATRX(NM_000489.3):c.485-5_594+5 -chrX 76949307 76949431 ATRX(NM_000489.3):c.371-5_484+5 -chrX 76952059 76952197 ATRX(NM_000489.3):c.243-5_370+5 -chrX 76953065 76953128 ATRX(NM_000489.3):c.190-5_242+5 -chrX 76954056 76954122 ATRX(NM_000489.3):c.134-5_189+5 -chrX 76972602 76972725 ATRX(NM_000489.3):c.21-5_133+5 -chrX 77041462 77041492 ATRX(NM_000489.3):c.-5_20+5 -chr1 27022889 27024036 ARID1A(NM_006015.4):c.-6_1137+5 -chr1 27056136 27056359 ARID1A(NM_006015.4):c.1138-5_1350+5 -chr1 27057637 27058100 ARID1A(NM_006015.4):c.1351-5_1803+5 -chr1 27059161 27059288 ARID1A(NM_006015.4):c.1804-5_1920+5 -chr1 27087341 27087592 ARID1A(NM_006015.4):c.1921-5_2161+5 -chr1 27087869 27087969 ARID1A(NM_006015.4):c.2162-5_2251+5 -chr1 27088637 27088815 ARID1A(NM_006015.4):c.2252-5_2419+5 -chr1 27089458 27089781 ARID1A(NM_006015.4):c.2420-5_2732+5 -chr1 27092706 27092862 ARID1A(NM_006015.4):c.2733-5_2878+5 -chr1 27092942 27093062 ARID1A(NM_006015.4):c.2879-5_2988+5 -chr1 27094275 27094495 ARID1A(NM_006015.4):c.2989-5_3198+5 -chr1 27097604 27097822 ARID1A(NM_006015.4):c.3199-5_3406+5 -chr1 27098985 27099128 ARID1A(NM_006015.4):c.3407-5_3539+5 -chr1 27099297 27099483 ARID1A(NM_006015.4):c.3540-5_3715+5 -chr1 27099831 27099992 ARID1A(NM_006015.4):c.3716-5_3866+5 -chr1 27100065 27100213 ARID1A(NM_006015.4):c.3867-5_4004+5 -chr1 27100287 27100394 ARID1A(NM_006015.4):c.4005-5_4101+5 -chr1 27100814 27101716 ARID1A(NM_006015.4):c.4102-5_4993+5 -chr1 27102062 27102203 ARID1A(NM_006015.4):c.4994-5_5124+5 -chr1 27105508 27107252 ARID1A(NM_006015.4):c.5125-5_*5 -chr1 115252201 115252204 NRAS(NM_002524.3):c.436_438 -chr1 115252288 115252291 NRAS(NM_002524.3):c.349_351 -chr1 115256527 115256530 NRAS(NM_002524.3):c.181_183 -chr1 115256533 115256536 NRAS(NM_002524.3):c.175_177 -chr1 115258742 115258748 NRAS(NM_002524.3):c.34_39 -chr1 226252133 226252136 H3F3A(NM_002107.4):c.82_84 -chr1 226252154 226252157 H3F3A(NM_002107.4):c.103_105 -chr2 209113110 209113113 IDH1(NM_005896.2):c.394_396 -chr3 178927968 178928131 PIK3CA(NM_006218.4):c.1252-5_1404+5(exon8) -chr3 178935992 178936127 PIK3CA(NM_006218.2):c.1540-5_1664+5 -chr3 178951876 178952157 PIK3CA(NM_006218.2):c.2937-5_*5 -chr4 55141002 55141145 PDGFRA(NM_006206.4):c.1654-5_1786+5 -chr4 55144057 55144178 PDGFRA(NM_006206.4):c.1892-5_2002+5 -chr4 55152002 55152135 PDGFRA(NM_006206.4):c.2440-5_2562+5 -chr4 55592017 55592221 KIT(NM_000222.2):c.1347-5_1540+5 -chr4 55593576 55593713 KIT(NM_000222.2):c.1648-5_1774+5 -chr4 55594171 55594292 KIT(NM_000222.2):c.1880-5_1990+5 -chr4 55595495 55595656 KIT(NM_000222.2):c.1991-5_2141+5 -chr4 55599230 55599363 KIT(NM_000222.2):c.2362-5_2484+5 -chr5 1295227 1295228 TERT(NM_198253.2):c.-124_-124 -chr5 1295249 1295250 TERT(NM_198253.2):c.-146_-146 -chr6 152265453 152265456 ESR1(NM_000125.3):c.907_909 -chr6 152332831 152332834 ESR1(NM_000125.3):c.1138_1140 -chr6 152332867 152332870 ESR1(NM_000125.3):c.1174_1176 -chr6 152415536 152415539 ESR1(NM_000125.3):c.1387_1389 -chr6 152419909 152419927 ESR1(NM_000125.3):c.1597_1614 -chr7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -chr7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -chr7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -chr7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -chr7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 -chr9 21968222 21968246 CDKN2A(NM_000077.3):c.*6_458-5 -chr9 21970895 21971212 CDKN2A(NM_000077.3):c.151-5_457+5 -chr9 21974671 21974831 CDKN2A(NM_000077.3):c.150+5_-5 -chr10 43609947 43609950 RET(NM_020975.4):c.1900_1902 -chr10 43617414 43617417 RET(NM_020975.4):c.2752_2754 -chr10 89624221 89624310 PTEN(NM_000314.4):c.-6_79+5 -chr10 89653776 89653871 PTEN(NM_000314.4):c.80-5_164+5 -chr10 89685264 89685319 PTEN(NM_000314.4):c.165-5_209+5 -chr10 89690797 89690851 PTEN(NM_000314.4):c.210-5_253+5 -chr10 89692764 89693013 PTEN(NM_000314.4):c.254-5_492+5 -chr10 89711869 89712021 PTEN(NM_000314.4):c.493-5_634+5 -chr10 89717604 89717781 PTEN(NM_000314.4):c.635-5_801+5 -chr10 89720645 89720880 PTEN(NM_000314.4):c.802-5_1026+5 -chr10 89725038 89725234 PTEN(NM_000314.4):c.1027-5_*5 -chr11 533872 533875 HRAS(NM_005343.2):c.181_183 -chr11 534283 534289 HRAS(NM_005343.2):c.34_39 -chr12 25378559 25378562 KRAS(NM_004985.3):c.436_438 -chr12 25378646 25378649 KRAS(NM_004985.3):c.349_351 -chr12 25380274 25380277 KRAS(NM_004985.3):c.181_183 -chr12 25380280 25380283 KRAS(NM_004985.3):c.175_177 -chr12 25398279 25398285 KRAS(NM_004985.3):c.34_39 -chr13 32890592 32890669 BRCA2(NM_000059.3):c.1-6_67+5 -chr13 32893208 32893467 BRCA2(NM_000059.3):c.68-5_316+5 -chr13 32899207 32899326 BRCA2(NM_000059.3):c.317-5_425+5 -chr13 32900232 32900292 BRCA2(NM_000059.3):c.426-5_475+5 -chr13 32900373 32900424 BRCA2(NM_000059.3):c.476-5_516+5 -chr13 32900630 32900755 BRCA2(NM_000059.3):c.517-5_631+5 -chr13 32903574 32903634 BRCA2(NM_000059.3):c.632-5_681+5 -chr13 32905050 32905172 BRCA2(NM_000059.3):c.682-5_793+5 -chr13 32906403 32907529 BRCA2(NM_000059.3):c.794-5_1909+5 -chr13 32910396 32915338 BRCA2(NM_000059.3):c.1910-5_6841+5 -chr13 32918689 32918795 BRCA2(NM_000059.3):c.6842-5_6937+5 -chr13 32920958 32921038 BRCA2(NM_000059.3):c.6938-5_7007+5 -chr13 32928992 32929430 BRCA2(NM_000059.3):c.7008-5_7435+5 -chr13 32930559 32930751 BRCA2(NM_000059.3):c.7436-5_7617+5 -chr13 32931873 32932071 BRCA2(NM_000059.3):c.7618-5_7805+5 -chr13 32936654 32936835 BRCA2(NM_000059.3):c.7806-5_7976+5 -chr13 32937310 32937675 BRCA2(NM_000059.3):c.7977-5_8331+5 -chr13 32944533 32944699 BRCA2(NM_000059.3):c.8332-5_8487+5 -chr13 32945087 32945242 BRCA2(NM_000059.3):c.8488-5_8632+5 -chr13 32950801 32950933 BRCA2(NM_000059.3):c.8633-5_8754+5 -chr13 32953448 32953657 BRCA2(NM_000059.3):c.8755-5_8953+5 -chr13 32953881 32954055 BRCA2(NM_000059.3):c.8954-5_9117+5 -chr13 32954138 32954287 BRCA2(NM_000059.3):c.9118-5_9256+5 -chr13 32968820 32969075 BRCA2(NM_000059.3):c.9257-5_9501+5 -chr13 32971029 32971186 BRCA2(NM_000059.3):c.9502-5_9648+5 -chr13 32972293 32972912 BRCA2(NM_000059.3):c.9649-5_*5 -chr15 90631836 90631839 IDH2(NM_002168.2):c.514_516 -chr17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5 -chr17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5 -chr17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T -chr17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5 -chr17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5 -chr17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5 -chr17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5 -chr17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5 -chr17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5 -chr17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5 -chr17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5 -chr17 37868206 37868209 ERBB2(NM_004448.2):c.928_930 -chr17 37879587 37879590 ERBB2(NM_004448.2):c.1963_1965 -chr17 37879656 37879659 ERBB2(NM_004448.2):c.2032_2034 -chr17 37880218 37880221 ERBB2(NM_004448.2):c.2263_2265 -chr17 37880254 37880257 ERBB2(NM_004448.2):c.2299_2301 -chr17 37880260 37880263 ERBB2(NM_004448.2):c.2305_2307 -chr17 37880999 37881002 ERBB2(NM_004448.2):c.2329_2331 -chr17 37881331 37881334 ERBB2(NM_004448.2):c.2524_2526 -chr17 37881615 37881618 ERBB2(NM_004448.2):c.2686_2688 -chr17 41197689 41197824 BRCA1(NM_007294.3):c.5468-5_*5 -chr17 41199654 41199725 BRCA1(NM_007294.3):c.5407-5_5467+5 -chr17 41201132 41201216 BRCA1(NM_007294.3):c.5333-5_5406+5 -chr17 41203074 41203139 BRCA1(NM_007294.3):c.5278-5_5332+5 -chr17 41209063 41209157 BRCA1(NM_007294.3):c.5194-5_5277+5 -chr17 41215344 41215395 BRCA1(NM_007294.3):c.5153-5_5193+5 -chr17 41215885 41215973 BRCA1(NM_007294.3):c.5075-5_5152+5 -chr17 41219619 41219717 BRCA1(NM_007294.3):c.4987-5_5074+5 -chr17 41222939 41223260 BRCA1(NM_007294.3):c.4676-5_4986+5 -chr17 41226342 41226543 BRCA1(NM_007294.3):c.4485-5_4675+5 -chr17 41228499 41228636 BRCA1(NM_007294.3):c.4358-5_4484+5 -chr17 41234415 41234597 BRCA1(NM_007294.3):c.4186-5_4357+5 -chr17 41242955 41243054 BRCA1(NM_007294.3):c.4097-5_4185+5 -chr17 41243446 41246882 BRCA1(NM_007294.3):c.671-5_4096+5 -chr17 41247857 41247944 BRCA1(NM_007294.3):c.594-5_670+5 -chr17 41249255 41249311 BRCA1(NM_007294.3):c.548-5_593+5 -chr17 41251786 41251902 BRCA1(NM_007294.3):c.442-5_547+5 -chr17 41256133 41256283 BRCA1(NM_007294.3):c.302-5_441+5 -chr17 41256879 41256978 BRCA1(NM_007294.3):c.213-5_301+5 -chr17 41258467 41258555 BRCA1(NM_007294.3):c.135-5_212+5 -chr17 41267737 41267801 BRCA1(NM_007294.3):c.81-5_134+5 -chr17 41276028 41276118 BRCA1(NM_007294.3):c.1-5_80+5 diff --git a/hotspot_coverage/Tumour_combined.groups b/hotspot_coverage/Tumour_combined.groups deleted file mode 100644 index 593b6b8..0000000 --- a/hotspot_coverage/Tumour_combined.groups +++ /dev/null @@ -1,186 +0,0 @@ -GENE -AR -AR -AR -AR -AR -AR -AR -AR -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -NRAS -NRAS -NRAS -NRAS -NRAS -H3F3A -H3F3A -IDH1 -PIK3CA -PIK3CA -PIK3CA -PDGFRA -PDGFRA -PDGFRA -KIT -KIT -KIT -KIT -KIT -TERT -TERT -ESR1 -ESR1 -ESR1 -ESR1 -ESR1 -EGFR -EGFR -EGFR -EGFR -BRAF -BRAF -CDKN2A -CDKN2A -CDKN2A -RET -RET -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -HRAS -HRAS -KRAS -KRAS -KRAS -KRAS -KRAS -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -IDH2 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -ERBB2 -ERBB2 -ERBB2 -ERBB2 -ERBB2 -ERBB2 -ERBB2 -ERBB2 -ERBB2 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 diff --git a/hotspot_coverage/Tumour_genescreen.bed b/hotspot_coverage/Tumour_genescreen.bed deleted file mode 100644 index ee11e1a..0000000 --- a/hotspot_coverage/Tumour_genescreen.bed +++ /dev/null @@ -1,134 +0,0 @@ -chrX 66764983 66766609 AR(NM_000044.2):c.-6_1616+5 -chrX 66863092 66863254 AR(NM_000044.2):c.1617-5_1768+5 -chrX 66905846 66905973 AR(NM_000044.2):c.1769-5_1885+5 -chrX 66931238 66931536 AR(NM_000044.2):c.1886-5_2173+5 -chrX 66937314 66937469 AR(NM_000044.2):c.2174-5_2318+5 -chrX 66941669 66941810 AR(NM_000044.2):c.2319-5_2449+5 -chrX 66942663 66942831 AR(NM_000044.2):c.2450-5_2607+5 -chrX 66943522 66943688 AR(NM_000044.2):c.2608-5_*5 -chrX 76763824 76764113 ATRX(NM_000489.3):c.7201-6_c*5 -chrX 76776260 76776399 ATRX(NM_000489.3):c.7072-5_7200+5 -chrX 76776875 76776981 ATRX(NM_000489.3):c.6976-5_7071+5 -chrX 76777735 76777871 ATRX(NM_000489.3):c.6850-5_6975+5 -chrX 76778724 76778884 ATRX(NM_000489.3):c.6700-5_6849+5 -chrX 76812916 76813121 ATRX(NM_000489.3):c.6505-5_6699+5 -chrX 76814134 76814322 ATRX(NM_000489.3):c.6327-5_6504+5 -chrX 76829709 76829828 ATRX(NM_000489.3):c.6218-5_6326+5 -chrX 76845298 76845415 ATRX(NM_000489.3):c.6111-5_6217+5 -chrX 76849160 76849324 ATRX(NM_000489.3):c.5957-5_6110+5 -chrX 76854874 76855054 ATRX(NM_000489.3):c.5787-5_5956+5 -chrX 76855195 76855294 ATRX(NM_000489.3):c.5698-5_5786+5 -chrX 76855897 76856038 ATRX(NM_000489.3):c.5567-5_5697+5 -chrX 76872075 76872203 ATRX(NM_000489.3):c.5449-5_5566+5 -chrX 76874268 76874454 ATRX(NM_000489.3):c.5273-5_5448+5 -chrX 76875857 76876005 ATRX(NM_000489.3):c.5135-5_5272+5 -chrX 76888689 76888877 ATRX(NM_000489.3):c.4957-5_5134+5 -chrX 76889048 76889205 ATRX(NM_000489.3):c.4810-5_4956+5 -chrX 76890079 76890199 ATRX(NM_000489.3):c.4700-5_4809+5 -chrX 76891400 76891552 ATRX(NM_000489.3):c.4558-5_4699+5 -chrX 76907598 76907848 ATRX(NM_000489.3):c.4318-5_4557+5 -chrX 76909582 76909695 ATRX(NM_000489.3):c.4215-5_4317+5 -chrX 76912044 76912148 ATRX(NM_000489.3):c.4121-5_4214+5 -chrX 76918865 76919052 ATRX(NM_000489.3):c.3944-5_4120+5 -chrX 76920128 76920272 ATRX(NM_000489.3):c.3810-5_3943+5 -chrX 76931715 76931798 ATRX(NM_000489.3):c.3737-5_3809+5 -chrX 76937006 76940090 ATRX(NM_000489.3):c.663-5_3736+5 -chrX 76940425 76940503 ATRX(NM_000489.3):c.595-5_662+5 -chrX 76944305 76944425 ATRX(NM_000489.3):c.485-5_594+5 -chrX 76949307 76949431 ATRX(NM_000489.3):c.371-5_484+5 -chrX 76952059 76952197 ATRX(NM_000489.3):c.243-5_370+5 -chrX 76953065 76953128 ATRX(NM_000489.3):c.190-5_242+5 -chrX 76954056 76954122 ATRX(NM_000489.3):c.134-5_189+5 -chrX 76972602 76972725 ATRX(NM_000489.3):c.21-5_133+5 -chrX 77041462 77041492 ATRX(NM_000489.3):c.-5_20+5 -chr1 27022889 27024036 ARID1A(NM_006015.4):c.-6_1137+5 -chr1 27056136 27056359 ARID1A(NM_006015.4):c.1138-5_1350+5 -chr1 27057637 27058100 ARID1A(NM_006015.4):c.1351-5_1803+5 -chr1 27059161 27059288 ARID1A(NM_006015.4):c.1804-5_1920+5 -chr1 27087341 27087592 ARID1A(NM_006015.4):c.1921-5_2161+5 -chr1 27087869 27087969 ARID1A(NM_006015.4):c.2162-5_2251+5 -chr1 27088637 27088815 ARID1A(NM_006015.4):c.2252-5_2419+5 -chr1 27089458 27089781 ARID1A(NM_006015.4):c.2420-5_2732+5 -chr1 27092706 27092862 ARID1A(NM_006015.4):c.2733-5_2878+5 -chr1 27092942 27093062 ARID1A(NM_006015.4):c.2879-5_2988+5 -chr1 27094275 27094495 ARID1A(NM_006015.4):c.2989-5_3198+5 -chr1 27097604 27097822 ARID1A(NM_006015.4):c.3199-5_3406+5 -chr1 27098985 27099128 ARID1A(NM_006015.4):c.3407-5_3539+5 -chr1 27099297 27099483 ARID1A(NM_006015.4):c.3540-5_3715+5 -chr1 27099831 27099992 ARID1A(NM_006015.4):c.3716-5_3866+5 -chr1 27100065 27100213 ARID1A(NM_006015.4):c.3867-5_4004+5 -chr1 27100287 27100394 ARID1A(NM_006015.4):c.4005-5_4101+5 -chr1 27100814 27101716 ARID1A(NM_006015.4):c.4102-5_4993+5 -chr1 27102062 27102203 ARID1A(NM_006015.4):c.4994-5_5124+5 -chr1 27105508 27107252 ARID1A(NM_006015.4):c.5125-5_*5 -chr9 21968222 21968246 CDKN2A(NM_000077.3):c.*6_458-5 -chr9 21970895 21971212 CDKN2A(NM_000077.3):c.151-5_457+5 -chr9 21974671 21974831 CDKN2A(NM_000077.3):c.150+5_-5 -chr10 89624221 89624310 PTEN(NM_000314.4):c.-6_79+5 -chr10 89653776 89653871 PTEN(NM_000314.4):c.80-5_164+5 -chr10 89685264 89685319 PTEN(NM_000314.4):c.165-5_209+5 -chr10 89690797 89690851 PTEN(NM_000314.4):c.210-5_253+5 -chr10 89692764 89693013 PTEN(NM_000314.4):c.254-5_492+5 -chr10 89711869 89712021 PTEN(NM_000314.4):c.493-5_634+5 -chr10 89717604 89717781 PTEN(NM_000314.4):c.635-5_801+5 -chr10 89720645 89720880 PTEN(NM_000314.4):c.802-5_1026+5 -chr10 89725038 89725234 PTEN(NM_000314.4):c.1027-5_*5 -chr13 32890592 32890669 BRCA2(NM_000059.3):c.1-6_67+5 -chr13 32893208 32893467 BRCA2(NM_000059.3):c.68-5_316+5 -chr13 32899207 32899326 BRCA2(NM_000059.3):c.317-5_425+5 -chr13 32900232 32900292 BRCA2(NM_000059.3):c.426-5_475+5 -chr13 32900373 32900424 BRCA2(NM_000059.3):c.476-5_516+5 -chr13 32900630 32900755 BRCA2(NM_000059.3):c.517-5_631+5 -chr13 32903574 32903634 BRCA2(NM_000059.3):c.632-5_681+5 -chr13 32905050 32905172 BRCA2(NM_000059.3):c.682-5_793+5 -chr13 32906403 32907529 BRCA2(NM_000059.3):c.794-5_1909+5 -chr13 32910396 32915338 BRCA2(NM_000059.3):c.1910-5_6841+5 -chr13 32918689 32918795 BRCA2(NM_000059.3):c.6842-5_6937+5 -chr13 32920958 32921038 BRCA2(NM_000059.3):c.6938-5_7007+5 -chr13 32928992 32929430 BRCA2(NM_000059.3):c.7008-5_7435+5 -chr13 32930559 32930751 BRCA2(NM_000059.3):c.7436-5_7617+5 -chr13 32931873 32932071 BRCA2(NM_000059.3):c.7618-5_7805+5 -chr13 32936654 32936835 BRCA2(NM_000059.3):c.7806-5_7976+5 -chr13 32937310 32937675 BRCA2(NM_000059.3):c.7977-5_8331+5 -chr13 32944533 32944699 BRCA2(NM_000059.3):c.8332-5_8487+5 -chr13 32945087 32945242 BRCA2(NM_000059.3):c.8488-5_8632+5 -chr13 32950801 32950933 BRCA2(NM_000059.3):c.8633-5_8754+5 -chr13 32953448 32953657 BRCA2(NM_000059.3):c.8755-5_8953+5 -chr13 32953881 32954055 BRCA2(NM_000059.3):c.8954-5_9117+5 -chr13 32954138 32954287 BRCA2(NM_000059.3):c.9118-5_9256+5 -chr13 32968820 32969075 BRCA2(NM_000059.3):c.9257-5_9501+5 -chr13 32971029 32971186 BRCA2(NM_000059.3):c.9502-5_9648+5 -chr13 32972293 32972912 BRCA2(NM_000059.3):c.9649-5_*5 -chr17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5 -chr17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5 -chr17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T -chr17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5 -chr17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5 -chr17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5 -chr17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5 -chr17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5 -chr17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5 -chr17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5 -chr17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5 -chr17 41197689 41197824 BRCA1(NM_007294.3):c.5468-5_*5 -chr17 41199654 41199725 BRCA1(NM_007294.3):c.5407-5_5467+5 -chr17 41201132 41201216 BRCA1(NM_007294.3):c.5333-5_5406+5 -chr17 41203074 41203139 BRCA1(NM_007294.3):c.5278-5_5332+5 -chr17 41209063 41209157 BRCA1(NM_007294.3):c.5194-5_5277+5 -chr17 41215344 41215395 BRCA1(NM_007294.3):c.5153-5_5193+5 -chr17 41215885 41215973 BRCA1(NM_007294.3):c.5075-5_5152+5 -chr17 41219619 41219717 BRCA1(NM_007294.3):c.4987-5_5074+5 -chr17 41222939 41223260 BRCA1(NM_007294.3):c.4676-5_4986+5 -chr17 41226342 41226543 BRCA1(NM_007294.3):c.4485-5_4675+5 -chr17 41228499 41228636 BRCA1(NM_007294.3):c.4358-5_4484+5 -chr17 41234415 41234597 BRCA1(NM_007294.3):c.4186-5_4357+5 -chr17 41242955 41243054 BRCA1(NM_007294.3):c.4097-5_4185+5 -chr17 41243446 41246882 BRCA1(NM_007294.3):c.671-5_4096+5 -chr17 41247857 41247944 BRCA1(NM_007294.3):c.594-5_670+5 -chr17 41249255 41249311 BRCA1(NM_007294.3):c.548-5_593+5 -chr17 41251786 41251902 BRCA1(NM_007294.3):c.442-5_547+5 -chr17 41256133 41256283 BRCA1(NM_007294.3):c.302-5_441+5 -chr17 41256879 41256978 BRCA1(NM_007294.3):c.213-5_301+5 -chr17 41258467 41258555 BRCA1(NM_007294.3):c.135-5_212+5 -chr17 41267737 41267801 BRCA1(NM_007294.3):c.81-5_134+5 -chr17 41276028 41276118 BRCA1(NM_007294.3):c.1-5_80+5 diff --git a/hotspot_coverage/Tumour_genescreen.groups b/hotspot_coverage/Tumour_genescreen.groups deleted file mode 100644 index 32fde46..0000000 --- a/hotspot_coverage/Tumour_genescreen.groups +++ /dev/null @@ -1,135 +0,0 @@ -GENE -AR -AR -AR -AR -AR -AR -AR -AR -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ATRX -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -ARID1A -CDKN2A -CDKN2A -CDKN2A -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -PTEN -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -BRCA2 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 -BRCA1 diff --git a/hotspot_coverage/Tumour_hotspots.bed b/hotspot_coverage/Tumour_hotspots.bed deleted file mode 100644 index b2d87af..0000000 --- a/hotspot_coverage/Tumour_hotspots.bed +++ /dev/null @@ -1,56 +0,0 @@ -chr1 115252201 115252204 NRAS(NM_002524.3):c.436_438 -chr1 115252288 115252291 NRAS(NM_002524.3):c.349_351 -chr1 115256527 115256530 NRAS(NM_002524.3):c.181_183 -chr1 115256533 115256536 NRAS(NM_002524.3):c.175_177 -chr1 115258742 115258748 NRAS(NM_002524.3):c.34_39 -chr1 226252133 226252136 H3F3A(NM_002107.4):c.82_84 -chr1 226252154 226252157 H3F3A(NM_002107.4):c.103_105 -chr2 209113110 209113113 IDH1(NM_005896.2):c.394_396 -chr3 178927968 178928131 PIK3CA(NM_006218.4):c.1252-5_1404+5(exon8) -chr3 178927979 178927982 PIK3CA(NM_006218.4):c.1258_1260(Cys420) -chr3 178935992 178936127 PIK3CA(NM_006218.2):c.1540-5_1664+5 -chr3 178936081 178936084 PIK3CA(NM_006218.4):c.1624_1626(Glu542) -chr3 178936090 178936093 PIK3CA(NM_006218.4):c.1633_1635(Glu545) -chr3 178936093 178936096 PIK3CA(NM_006218.4):c.1636_1638(Gln546) -chr3 178951876 178952157 PIK3CA(NM_006218.2):c.2937-5_*5 -chr3 178952083 178952086 PIK3CA(NM_006218.4):c.3139_3141(His1047) -chr4 55141002 55141145 PDGFRA(NM_006206.4):c.1654-5_1786+5 -chr4 55144057 55144178 PDGFRA(NM_006206.4):c.1892-5_2002+5 -chr4 55152002 55152135 PDGFRA(NM_006206.4):c.2440-5_2562+5 -chr4 55592017 55592221 KIT(NM_000222.2):c.1347-5_1540+5 -chr4 55593576 55593713 KIT(NM_000222.2):c.1648-5_1774+5 -chr4 55594171 55594292 KIT(NM_000222.2):c.1880-5_1990+5 -chr4 55595495 55595656 KIT(NM_000222.2):c.1991-5_2141+5 -chr4 55599230 55599363 KIT(NM_000222.2):c.2362-5_2484+5 -chr5 1295227 1295228 TERT(NM_198253.2):c.-124_-124 -chr5 1295249 1295250 TERT(NM_198253.2):c.-146_-146 -chr6 152265453 152265456 ESR1(NM_000125.3):c.907_909 -chr6 152332831 152332834 ESR1(NM_000125.3):c.1138_1140 -chr6 152332867 152332870 ESR1(NM_000125.3):c.1174_1176 -chr6 152415536 152415539 ESR1(NM_000125.3):c.1387_1389 -chr6 152419909 152419927 ESR1(NM_000125.3):c.1597_1614 -chr7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -chr7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -chr7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -chr7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -chr7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -chr7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 -chr10 43609947 43609950 RET(NM_020975.4):c.1900_1902 -chr10 43617414 43617417 RET(NM_020975.4):c.2752_2754 -chr11 533872 533875 HRAS(NM_005343.2):c.181_183 -chr11 534283 534289 HRAS(NM_005343.2):c.34_39 -chr12 25378559 25378562 KRAS(NM_004985.3):c.436_438 -chr12 25378646 25378649 KRAS(NM_004985.3):c.349_351 -chr12 25380274 25380277 KRAS(NM_004985.3):c.181_183 -chr12 25380280 25380283 KRAS(NM_004985.3):c.175_177 -chr12 25398279 25398285 KRAS(NM_004985.3):c.34_39 -chr15 90631836 90631839 IDH2(NM_002168.2):c.514_516 -chr17 37868206 37868209 ERBB2(NM_004448.2):c.928_930 -chr17 37879587 37879590 ERBB2(NM_004448.2):c.1963_1965 -chr17 37879656 37879659 ERBB2(NM_004448.2):c.2032_2034 -chr17 37880218 37880221 ERBB2(NM_004448.2):c.2263_2265 -chr17 37880254 37880257 ERBB2(NM_004448.2):c.2299_2301 -chr17 37880260 37880263 ERBB2(NM_004448.2):c.2305_2307 -chr17 37880999 37881002 ERBB2(NM_004448.2):c.2329_2331 -chr17 37881331 37881334 ERBB2(NM_004448.2):c.2524_2526 -chr17 37881615 37881618 ERBB2(NM_004448.2):c.2686_2688 diff --git a/hotspot_coverage/Tumour_hotspots.groups b/hotspot_coverage/Tumour_hotspots.groups deleted file mode 100644 index ebbe93f..0000000 --- a/hotspot_coverage/Tumour_hotspots.groups +++ /dev/null @@ -1,57 +0,0 @@ -GENE -NRAS -NRAS -NRAS -NRAS -NRAS -H3F3A -H3F3A -IDH1 -PIK3CA -PIK3CA -PIK3CA -PIK3CA -PIK3CA -PIK3CA -PIK3CA -PIK3CA -PDGFRA -PDGFRA -PDGFRA -KIT -KIT -KIT -KIT -KIT -TERT -TERT -ESR1 -ESR1 -ESR1 -ESR1 -ESR1 -EGFR -EGFR -EGFR -EGFR -BRAF -BRAF -RET -RET -HRAS -HRAS -KRAS -KRAS -KRAS -KRAS -KRAS -IDH2 -ERBB2 -ERBB2 -ERBB2 -ERBB2 -ERBB2 -ERBB2 -ERBB2 -ERBB2 -ERBB2 diff --git a/hotspot_coverage/aitcl_combined.bed b/hotspot_coverage/aitcl_combined.bed deleted file mode 100644 index 74dfa09..0000000 --- a/hotspot_coverage/aitcl_combined.bed +++ /dev/null @@ -1,35 +0,0 @@ -chr2 25457142 25457294 DNMT3A(NM_175629.2):exon_23 -chr2 25458570 25458699 DNMT3A(NM_175629.2):exon_22 -chr2 25459799 25459879 DNMT3A(NM_175629.2):exon_21 -chr2 25461993 25462089 DNMT3A(NM_175629.2):exon_20 -chr2 25463165 25463324 DNMT3A(NM_175629.2):exon_19 -chr2 25463503 25463604 DNMT3A(NM_175629.2):exon_18 -chr2 25464425 25464581 DNMT3A(NM_175629.2):exon_17 -chr2 25466761 25466856 DNMT3A(NM_175629.2):exon_16 -chr2 25467018 25467212 DNMT3A(NM_175629.2):exon_15 -chr2 25467403 25467526 DNMT3A(NM_175629.2):exon_14 -chr2 25468116 25468206 DNMT3A(NM_175629.2):exon_13 -chr2 25468883 25468938 DNMT3A(NM_175629.2):exon_12 -chr2 25469023 25469183 DNMT3A(NM_175629.2):exon_11 -chr2 25469483 25469650 DNMT3A(NM_175629.2):exon_10 -chr2 25469914 25470032 DNMT3A(NM_175629.2):exon_9 -chr2 25470454 25470623 DNMT3A(NM_175629.2):exon_8 -chr2 25470900 25471126 DNMT3A(NM_175629.2):exon_7 -chr2 25472520 25472598 DNMT3A(NM_153759.3):exon_2 -chr2 25475057 25475071 DNMT3A(NM_153759.3):exon_1 -chr2 25497804 25497961 DNMT3A(NM_175629.2):exon_6 -chr2 25498363 25498417 DNMT3A(NM_175629.2):exon_5 -chr2 25505304 25505585 DNMT3A(NM_175629.2):exon_4 -chr2 25523002 25523117 DNMT3A(NM_175629.2):exon_3 -chr2 25536776 25536858 DNMT3A(NM_175629.2):exon_2 -chr3 49412861 49413027 RHOA(NM_001664.3):exon_2 -chr4 106155094 106158602 TET2(NM_001127208.2):exon_3 -chr4 106162490 106162591 TET2(NM_001127208.2):exon_4 -chr4 106163985 106164089 TET2(NM_001127208.2):exon_5 -chr4 106164721 106164940 TET2(NM_001127208.2):exon_6 -chr4 106180770 106180931 TET2(NM_001127208.2):exon_7 -chr4 106182910 106183010 TET2(NM_001127208.2):exon_8 -chr4 106190761 106190909 TET2(NM_001127208.2):exon_9 -chr4 106193715 106194080 TET2(NM_001127208.2):exon_10 -chr4 106196199 106197681 TET2(NM_001127208.2):exon_11 -chr15 90631813 90631984 IDH2(NM_002168.3):exon_4 diff --git a/hotspot_coverage/aitcl_combined.groups b/hotspot_coverage/aitcl_combined.groups deleted file mode 100644 index e665928..0000000 --- a/hotspot_coverage/aitcl_combined.groups +++ /dev/null @@ -1,36 +0,0 @@ -GENE -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -RHOA -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -IDH2 diff --git a/hotspot_coverage/aitcl_genescreen.bed b/hotspot_coverage/aitcl_genescreen.bed deleted file mode 100644 index 74dfa09..0000000 --- a/hotspot_coverage/aitcl_genescreen.bed +++ /dev/null @@ -1,35 +0,0 @@ -chr2 25457142 25457294 DNMT3A(NM_175629.2):exon_23 -chr2 25458570 25458699 DNMT3A(NM_175629.2):exon_22 -chr2 25459799 25459879 DNMT3A(NM_175629.2):exon_21 -chr2 25461993 25462089 DNMT3A(NM_175629.2):exon_20 -chr2 25463165 25463324 DNMT3A(NM_175629.2):exon_19 -chr2 25463503 25463604 DNMT3A(NM_175629.2):exon_18 -chr2 25464425 25464581 DNMT3A(NM_175629.2):exon_17 -chr2 25466761 25466856 DNMT3A(NM_175629.2):exon_16 -chr2 25467018 25467212 DNMT3A(NM_175629.2):exon_15 -chr2 25467403 25467526 DNMT3A(NM_175629.2):exon_14 -chr2 25468116 25468206 DNMT3A(NM_175629.2):exon_13 -chr2 25468883 25468938 DNMT3A(NM_175629.2):exon_12 -chr2 25469023 25469183 DNMT3A(NM_175629.2):exon_11 -chr2 25469483 25469650 DNMT3A(NM_175629.2):exon_10 -chr2 25469914 25470032 DNMT3A(NM_175629.2):exon_9 -chr2 25470454 25470623 DNMT3A(NM_175629.2):exon_8 -chr2 25470900 25471126 DNMT3A(NM_175629.2):exon_7 -chr2 25472520 25472598 DNMT3A(NM_153759.3):exon_2 -chr2 25475057 25475071 DNMT3A(NM_153759.3):exon_1 -chr2 25497804 25497961 DNMT3A(NM_175629.2):exon_6 -chr2 25498363 25498417 DNMT3A(NM_175629.2):exon_5 -chr2 25505304 25505585 DNMT3A(NM_175629.2):exon_4 -chr2 25523002 25523117 DNMT3A(NM_175629.2):exon_3 -chr2 25536776 25536858 DNMT3A(NM_175629.2):exon_2 -chr3 49412861 49413027 RHOA(NM_001664.3):exon_2 -chr4 106155094 106158602 TET2(NM_001127208.2):exon_3 -chr4 106162490 106162591 TET2(NM_001127208.2):exon_4 -chr4 106163985 106164089 TET2(NM_001127208.2):exon_5 -chr4 106164721 106164940 TET2(NM_001127208.2):exon_6 -chr4 106180770 106180931 TET2(NM_001127208.2):exon_7 -chr4 106182910 106183010 TET2(NM_001127208.2):exon_8 -chr4 106190761 106190909 TET2(NM_001127208.2):exon_9 -chr4 106193715 106194080 TET2(NM_001127208.2):exon_10 -chr4 106196199 106197681 TET2(NM_001127208.2):exon_11 -chr15 90631813 90631984 IDH2(NM_002168.3):exon_4 diff --git a/hotspot_coverage/aitcl_genescreen.groups b/hotspot_coverage/aitcl_genescreen.groups deleted file mode 100644 index e665928..0000000 --- a/hotspot_coverage/aitcl_genescreen.groups +++ /dev/null @@ -1,36 +0,0 @@ -GENE -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -RHOA -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -IDH2 diff --git a/hotspot_coverage/aitcl_hotspots.bed b/hotspot_coverage/aitcl_hotspots.bed deleted file mode 100644 index ae8c3f6..0000000 --- a/hotspot_coverage/aitcl_hotspots.bed +++ /dev/null @@ -1,4 +0,0 @@ -chr3 49412971 49412974 RHOA(NM_001664.3):codon_G17 -chr3 49412968 49412971 RHOA(NM_001664.3):codon_K18 -chr3 49412965 49412968 RHOA(NM_001664.3):codon_T19 -chr15 90631836 90631839 IDH2(NM_002168.3):codon_R172 diff --git a/hotspot_coverage/aitcl_hotspots.groups b/hotspot_coverage/aitcl_hotspots.groups deleted file mode 100644 index 20bb3e9..0000000 --- a/hotspot_coverage/aitcl_hotspots.groups +++ /dev/null @@ -1,5 +0,0 @@ -GENE -RHOA -RHOA -RHOA -IDH2 diff --git a/hotspot_coverage/aml_combined.bed b/hotspot_coverage/aml_combined.bed deleted file mode 100644 index 92f05cf..0000000 --- a/hotspot_coverage/aml_combined.bed +++ /dev/null @@ -1,17 +0,0 @@ -chr2 209113104 209113119 IDH1(NM_005896.3):codon_R132 -chr5 170837525 170837574 NPM1(NM_002520.6):exon_11 -chr13 28592598 28592731 FLT3(NM_004119.2):exon_20 -chr13 28608018 28608133 FLT3(NM_004119.2):exon_15 -chr13 28608213 28608356 FLT3(NM_004119.2):exon_14 -chr13 28608432 28608549 FLT3(NM_004119.2):exon_13 -chr15 90631813 90631984 IDH2(NM_002168.3):exon_4 -chr17 7572921 7573013 TP53(NM_000546.5):exon_11 -chr17 7573921 7574038 TP53(NM_000546.5):exon_10 -chr17 7576847 7576931 TP53(NM_000546.5):exon_9 -chr17 7577013 7577160 TP53(NM_000546.5):exon_8 -chr17 7577493 7577613 TP53(NM_000546.5):exon_7 -chr17 7578171 7578294 TP53(NM_000546.5):exon_6 -chr17 7578365 7578559 TP53(NM_000546.5):exon_5 -chr17 7579306 7579595 TP53(NM_000546.5):exon_4 -chr17 7579694 7579726 TP53(NM_000546.5):exon_3 -chr17 7579833 7579917 TP53(NM_000546.5):exon_2 diff --git a/hotspot_coverage/aml_combined.groups b/hotspot_coverage/aml_combined.groups deleted file mode 100644 index a306af8..0000000 --- a/hotspot_coverage/aml_combined.groups +++ /dev/null @@ -1,18 +0,0 @@ -GENE -IDH1 -NPM1 -FLT3 -FLT3 -FLT3 -FLT3 -IDH2 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 diff --git a/hotspot_coverage/aml_genescreen.bed b/hotspot_coverage/aml_genescreen.bed deleted file mode 100644 index 92f05cf..0000000 --- a/hotspot_coverage/aml_genescreen.bed +++ /dev/null @@ -1,17 +0,0 @@ -chr2 209113104 209113119 IDH1(NM_005896.3):codon_R132 -chr5 170837525 170837574 NPM1(NM_002520.6):exon_11 -chr13 28592598 28592731 FLT3(NM_004119.2):exon_20 -chr13 28608018 28608133 FLT3(NM_004119.2):exon_15 -chr13 28608213 28608356 FLT3(NM_004119.2):exon_14 -chr13 28608432 28608549 FLT3(NM_004119.2):exon_13 -chr15 90631813 90631984 IDH2(NM_002168.3):exon_4 -chr17 7572921 7573013 TP53(NM_000546.5):exon_11 -chr17 7573921 7574038 TP53(NM_000546.5):exon_10 -chr17 7576847 7576931 TP53(NM_000546.5):exon_9 -chr17 7577013 7577160 TP53(NM_000546.5):exon_8 -chr17 7577493 7577613 TP53(NM_000546.5):exon_7 -chr17 7578171 7578294 TP53(NM_000546.5):exon_6 -chr17 7578365 7578559 TP53(NM_000546.5):exon_5 -chr17 7579306 7579595 TP53(NM_000546.5):exon_4 -chr17 7579694 7579726 TP53(NM_000546.5):exon_3 -chr17 7579833 7579917 TP53(NM_000546.5):exon_2 diff --git a/hotspot_coverage/aml_genescreen.groups b/hotspot_coverage/aml_genescreen.groups deleted file mode 100644 index a306af8..0000000 --- a/hotspot_coverage/aml_genescreen.groups +++ /dev/null @@ -1,18 +0,0 @@ -GENE -IDH1 -NPM1 -FLT3 -FLT3 -FLT3 -FLT3 -IDH2 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 diff --git a/hotspot_coverage/breast_combined.bed b/hotspot_coverage/breast_combined.bed deleted file mode 100644 index af1299b..0000000 --- a/hotspot_coverage/breast_combined.bed +++ /dev/null @@ -1,3 +0,0 @@ -chr3 178927968 178928131 PIK3CA(NM_006218.4):c.1252-5_1404+5(exon8) -chr3 178935992 178936127 PIK3CA(NM_006218.4):c.1540-5_1664+5(exon10) -chr3 178951876 178952157 PIK3CA(NM_006218.4):c.2937-5_3207+5(exon21) diff --git a/hotspot_coverage/breast_combined.groups b/hotspot_coverage/breast_combined.groups deleted file mode 100644 index 7f8d49c..0000000 --- a/hotspot_coverage/breast_combined.groups +++ /dev/null @@ -1,4 +0,0 @@ -GENE -PIK3CA -PIK3CA -PIK3CA diff --git a/hotspot_coverage/breast_hotspots.bed b/hotspot_coverage/breast_hotspots.bed deleted file mode 100644 index c1746c5..0000000 --- a/hotspot_coverage/breast_hotspots.bed +++ /dev/null @@ -1,8 +0,0 @@ -chr3 178927968 178928131 PIK3CA(NM_006218.4):c.1252-5_1404+5(exon8) -chr3 178927979 178927982 PIK3CA(NM_006218.4):c.1258_1260(Cys420) -chr3 178935992 178936127 PIK3CA(NM_006218.4):c.1540-5_1664+5(exon10) -chr3 178936081 178936084 PIK3CA(NM_006218.4):c.1624_1626(Glu542) -chr3 178936090 178936093 PIK3CA(NM_006218.4):c.1633_1635(Glu545) -chr3 178936093 178936096 PIK3CA(NM_006218.4):c.1636_1638(Gln546) -chr3 178951876 178952157 PIK3CA(NM_006218.4):c.2937-5_3207+5(exon21) -chr3 178952083 178952086 PIK3CA(NM_006218.4):c.3139_3141(His1047) diff --git a/hotspot_coverage/breast_hotspots.groups b/hotspot_coverage/breast_hotspots.groups deleted file mode 100644 index ccb0a3f..0000000 --- a/hotspot_coverage/breast_hotspots.groups +++ /dev/null @@ -1,9 +0,0 @@ -GENE -PIK3CA -PIK3CA -PIK3CA -PIK3CA -PIK3CA -PIK3CA -PIK3CA -PIK3CA diff --git a/hotspot_coverage/cll_combined.bed b/hotspot_coverage/cll_combined.bed deleted file mode 100644 index f72e3e9..0000000 --- a/hotspot_coverage/cll_combined.bed +++ /dev/null @@ -1,10 +0,0 @@ -chr17 7572921 7573013 TP53(NM_000546.5):exon_11 -chr17 7573921 7574038 TP53(NM_000546.5):exon_10 -chr17 7576847 7576931 TP53(NM_000546.5):exon_9 -chr17 7577013 7577160 TP53(NM_000546.5):exon_8 -chr17 7577493 7577613 TP53(NM_000546.5):exon_7 -chr17 7578171 7578294 TP53(NM_000546.5):exon_6 -chr17 7578365 7578559 TP53(NM_000546.5):exon_5 -chr17 7579306 7579595 TP53(NM_000546.5):exon_4 -chr17 7579694 7579726 TP53(NM_000546.5):exon_3 -chr17 7579833 7579917 TP53(NM_000546.5):exon_2 diff --git a/hotspot_coverage/cll_combined.groups b/hotspot_coverage/cll_combined.groups deleted file mode 100644 index 82b7f21..0000000 --- a/hotspot_coverage/cll_combined.groups +++ /dev/null @@ -1,11 +0,0 @@ -GENE -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 diff --git a/hotspot_coverage/cll_genescreen.bed b/hotspot_coverage/cll_genescreen.bed deleted file mode 100644 index f72e3e9..0000000 --- a/hotspot_coverage/cll_genescreen.bed +++ /dev/null @@ -1,10 +0,0 @@ -chr17 7572921 7573013 TP53(NM_000546.5):exon_11 -chr17 7573921 7574038 TP53(NM_000546.5):exon_10 -chr17 7576847 7576931 TP53(NM_000546.5):exon_9 -chr17 7577013 7577160 TP53(NM_000546.5):exon_8 -chr17 7577493 7577613 TP53(NM_000546.5):exon_7 -chr17 7578171 7578294 TP53(NM_000546.5):exon_6 -chr17 7578365 7578559 TP53(NM_000546.5):exon_5 -chr17 7579306 7579595 TP53(NM_000546.5):exon_4 -chr17 7579694 7579726 TP53(NM_000546.5):exon_3 -chr17 7579833 7579917 TP53(NM_000546.5):exon_2 diff --git a/hotspot_coverage/cll_genescreen.groups b/hotspot_coverage/cll_genescreen.groups deleted file mode 100644 index 82b7f21..0000000 --- a/hotspot_coverage/cll_genescreen.groups +++ /dev/null @@ -1,11 +0,0 @@ -GENE -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 diff --git a/hotspot_coverage/endometrial-pole-tp53_combined.bed b/hotspot_coverage/endometrial-pole-tp53_combined.bed deleted file mode 100644 index 88f4af7..0000000 --- a/hotspot_coverage/endometrial-pole-tp53_combined.bed +++ /dev/null @@ -1,17 +0,0 @@ -chr12 133249744 133249868 POLE(NM006231.3):c.1473+5_c.1360-5(exon14) -chr12 133250155 133250298 POLE(NM006231.3):c.1359+5_c.1227-5(exon13) -chr12 133251978 133252108 POLE(NM006231.3):c.1226+5_c.1107-5(exon12) -chr12 133252315 133252411 POLE(NM006231.3):c.1106+5_c.1021-5(exon11) -chr12 133252674 133252795 POLE(NM006231.3):c.1020+5_c.910-5(exon10) -chr12 133253126 133253244 POLE(NM006231.3):c.909+5_c.802-5(exon9) -chr17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5(exon11) -chr17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5(exon10) -chr17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T(exon10alt) -chr17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5(exon9) -chr17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5(exon8) -chr17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5(exon7) -chr17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5(exon6) -chr17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5(exon5) -chr17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5(exon4) -chr17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5(exon3) -chr17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5(exon2) diff --git a/hotspot_coverage/endometrial-pole-tp53_combined.groups b/hotspot_coverage/endometrial-pole-tp53_combined.groups deleted file mode 100644 index 804b3fe..0000000 --- a/hotspot_coverage/endometrial-pole-tp53_combined.groups +++ /dev/null @@ -1,18 +0,0 @@ -GENE -POLE -POLE -POLE -POLE -POLE -POLE -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 diff --git a/hotspot_coverage/endometrial-pole-tp53_genescreen.bed b/hotspot_coverage/endometrial-pole-tp53_genescreen.bed deleted file mode 100644 index 88f4af7..0000000 --- a/hotspot_coverage/endometrial-pole-tp53_genescreen.bed +++ /dev/null @@ -1,17 +0,0 @@ -chr12 133249744 133249868 POLE(NM006231.3):c.1473+5_c.1360-5(exon14) -chr12 133250155 133250298 POLE(NM006231.3):c.1359+5_c.1227-5(exon13) -chr12 133251978 133252108 POLE(NM006231.3):c.1226+5_c.1107-5(exon12) -chr12 133252315 133252411 POLE(NM006231.3):c.1106+5_c.1021-5(exon11) -chr12 133252674 133252795 POLE(NM006231.3):c.1020+5_c.910-5(exon10) -chr12 133253126 133253244 POLE(NM006231.3):c.909+5_c.802-5(exon9) -chr17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5(exon11) -chr17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5(exon10) -chr17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T(exon10alt) -chr17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5(exon9) -chr17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5(exon8) -chr17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5(exon7) -chr17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5(exon6) -chr17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5(exon5) -chr17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5(exon4) -chr17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5(exon3) -chr17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5(exon2) diff --git a/hotspot_coverage/endometrial-pole-tp53_genescreen.groups b/hotspot_coverage/endometrial-pole-tp53_genescreen.groups deleted file mode 100644 index 804b3fe..0000000 --- a/hotspot_coverage/endometrial-pole-tp53_genescreen.groups +++ /dev/null @@ -1,18 +0,0 @@ -GENE -POLE -POLE -POLE -POLE -POLE -POLE -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 diff --git a/hotspot_coverage/endometrial-pole-tp53_hotspots.bed b/hotspot_coverage/endometrial-pole-tp53_hotspots.bed deleted file mode 100644 index 5e46052..0000000 --- a/hotspot_coverage/endometrial-pole-tp53_hotspots.bed +++ /dev/null @@ -1,11 +0,0 @@ -chr12 133249846 133249847 POLE(NM006231.3):c.1376_p.(Ser459Phe) -chr12 133249856 133249857 POLE(NM006231.3):c.1366_p.(Ala456Pro) -chr12 133250188 133250189 POLE(NM006231.3):c.1331_p.(Met444Lys) -chr12 133250212 133250213 POLE(NM006231.3):c.1307_p.(Pro436Arg) -chr12 133250249 133250250 POLE(NM006231.3):c.1270_p.(Leu424Ile) -chr12 133250288 133250289 POLE(NM006231.3):c.1231_p.(Val411Leu) -chr12 133252324 133252325 POLE(NM006231.3):c.1102_p.(Asp368Tyr) -chr12 133252326 133252327 POLE(NM006231.3):c.1100_p.(Phe367Ser) -chr12 133253150 133253151 POLE(NM006231.3):c.890_p.(Ser297Phe) -chr12 133253156 133253157 POLE(NM006231.3):c.884_p.(Met295Arg) -chr12 133253183 133253184 POLE(NM006231.3):c.857_p.(Pro286Arg) diff --git a/hotspot_coverage/endometrial-pole-tp53_hotspots.groups b/hotspot_coverage/endometrial-pole-tp53_hotspots.groups deleted file mode 100644 index a82e8be..0000000 --- a/hotspot_coverage/endometrial-pole-tp53_hotspots.groups +++ /dev/null @@ -1,12 +0,0 @@ -GENE -POLE -POLE -POLE -POLE -POLE -POLE -POLE -POLE -POLE -POLE -POLE diff --git a/hotspot_coverage/endometrial-pole_combined.bed b/hotspot_coverage/endometrial-pole_combined.bed deleted file mode 100644 index 529604c..0000000 --- a/hotspot_coverage/endometrial-pole_combined.bed +++ /dev/null @@ -1,6 +0,0 @@ -chr12 133249744 133249868 POLE(NM006231.3):c.1473+5_c.1360-5(exon14) -chr12 133250155 133250298 POLE(NM006231.3):c.1359+5_c.1227-5(exon13) -chr12 133251978 133252108 POLE(NM006231.3):c.1226+5_c.1107-5(exon12) -chr12 133252315 133252411 POLE(NM006231.3):c.1106+5_c.1021-5(exon11) -chr12 133252674 133252795 POLE(NM006231.3):c.1020+5_c.910-5(exon10) -chr12 133253126 133253244 POLE(NM006231.3):c.909+5_c.802-5(exon9) diff --git a/hotspot_coverage/endometrial-pole_combined.groups b/hotspot_coverage/endometrial-pole_combined.groups deleted file mode 100644 index 97cd508..0000000 --- a/hotspot_coverage/endometrial-pole_combined.groups +++ /dev/null @@ -1,7 +0,0 @@ -GENE -POLE -POLE -POLE -POLE -POLE -POLE diff --git a/hotspot_coverage/endometrial-pole_genescreen.bed b/hotspot_coverage/endometrial-pole_genescreen.bed deleted file mode 100644 index 529604c..0000000 --- a/hotspot_coverage/endometrial-pole_genescreen.bed +++ /dev/null @@ -1,6 +0,0 @@ -chr12 133249744 133249868 POLE(NM006231.3):c.1473+5_c.1360-5(exon14) -chr12 133250155 133250298 POLE(NM006231.3):c.1359+5_c.1227-5(exon13) -chr12 133251978 133252108 POLE(NM006231.3):c.1226+5_c.1107-5(exon12) -chr12 133252315 133252411 POLE(NM006231.3):c.1106+5_c.1021-5(exon11) -chr12 133252674 133252795 POLE(NM006231.3):c.1020+5_c.910-5(exon10) -chr12 133253126 133253244 POLE(NM006231.3):c.909+5_c.802-5(exon9) diff --git a/hotspot_coverage/endometrial-pole_genescreen.groups b/hotspot_coverage/endometrial-pole_genescreen.groups deleted file mode 100644 index 97cd508..0000000 --- a/hotspot_coverage/endometrial-pole_genescreen.groups +++ /dev/null @@ -1,7 +0,0 @@ -GENE -POLE -POLE -POLE -POLE -POLE -POLE diff --git a/hotspot_coverage/endometrial-pole_hotspots.bed b/hotspot_coverage/endometrial-pole_hotspots.bed deleted file mode 100644 index 5e46052..0000000 --- a/hotspot_coverage/endometrial-pole_hotspots.bed +++ /dev/null @@ -1,11 +0,0 @@ -chr12 133249846 133249847 POLE(NM006231.3):c.1376_p.(Ser459Phe) -chr12 133249856 133249857 POLE(NM006231.3):c.1366_p.(Ala456Pro) -chr12 133250188 133250189 POLE(NM006231.3):c.1331_p.(Met444Lys) -chr12 133250212 133250213 POLE(NM006231.3):c.1307_p.(Pro436Arg) -chr12 133250249 133250250 POLE(NM006231.3):c.1270_p.(Leu424Ile) -chr12 133250288 133250289 POLE(NM006231.3):c.1231_p.(Val411Leu) -chr12 133252324 133252325 POLE(NM006231.3):c.1102_p.(Asp368Tyr) -chr12 133252326 133252327 POLE(NM006231.3):c.1100_p.(Phe367Ser) -chr12 133253150 133253151 POLE(NM006231.3):c.890_p.(Ser297Phe) -chr12 133253156 133253157 POLE(NM006231.3):c.884_p.(Met295Arg) -chr12 133253183 133253184 POLE(NM006231.3):c.857_p.(Pro286Arg) diff --git a/hotspot_coverage/endometrial-pole_hotspots.groups b/hotspot_coverage/endometrial-pole_hotspots.groups deleted file mode 100644 index a82e8be..0000000 --- a/hotspot_coverage/endometrial-pole_hotspots.groups +++ /dev/null @@ -1,12 +0,0 @@ -GENE -POLE -POLE -POLE -POLE -POLE -POLE -POLE -POLE -POLE -POLE -POLE diff --git a/hotspot_coverage/fight-209_combined.bed b/hotspot_coverage/fight-209_combined.bed deleted file mode 100644 index 1887089..0000000 --- a/hotspot_coverage/fight-209_combined.bed +++ /dev/null @@ -1,49 +0,0 @@ -chr4 1803245 1803248 FGFR3(NM_000142.4):codon_R200 -chr4 1803563 1803566 FGFR3(NM_000142.4):codon_R248 -chr4 1803566 1803569 FGFR3(NM_000142.4):codon_S249 -chr4 1805511 1805514 FGFR3(NM_000142.4):codon_G342 -chr4 1806056 1806247 FGFR3(NM_000142.4):exon_9 -chr4 1807332 1807335 FGFR3(NM_000142.4):codon_M528 -chr4 1807368 1807371 FGFR3(NM_000142.4):codon_N540 -chr4 1807493 1807496 FGFR3(NM_000142.4):codon_V555 -chr4 1807801 1807804 FGFR3(NM_000142.4):codon_R621 -chr4 1807861 1807864 FGFR3(NM_000142.4):codon_D641 -chr4 1807888 1807891 FGFR3(NM_000142.4):codon_K650 -chr8 38285492 38285495 FGFR1(NM_023110.2):codon_R189 -chr8 38282206 38282209 FGFR1(NM_023110.2):codon_P252 -chr8 38277212 38277215 FGFR1(NM_023110.2):codon_Y374 -chr8 38277191 38277194 FGFR1(NM_023110.2):codon_C381 -chr8 38275840 38275843 FGFR1(NM_023110.2):codon_R445 -chr8 38274848 38274851 FGFR1(NM_023110.2):codon_N546 -chr8 38273558 38273561 FGFR1(NM_023110.2):codon_V561 -chr8 38272305 38272308 FGFR1(NM_023110.2):codon_K656 -chr10 123310899 123310929 FGFR2(NM_000141.4):exon_5_partial_p167-176 -chr10 123310818 123310821 FGFR2(NM_000141.4):codon_R203 -chr10 123298223 123298226 FGFR2(NM_000141.4):codon_R210 -chr10 123279675 123279678 FGFR2(NM_000141.4):codon_S252 -chr10 123279672 123279675 FGFR2(NM_000141.4):codon_P253 -chr10 123279612 123279666 FGFR2(NM_000141.4):exon_7_partial_p256-273 -chr10 123279495 123279594 FGFR2(NM_000141.4):exon_7_partial_p280-312 -chr10 123276971 123276974 FGFR2(NM_000141.4):codon_A315 -chr10 123276908 123276911 FGFR2(NM_000141.4):codon_D336 -chr10 123276890 123276893 FGFR2(NM_000141.4):codon_C342 -chr10 123276875 123276878 FGFR2(NM_000141.4):codon_S347 -chr10 123276863 123276866 FGFR2(NM_000141.4):codon_S351 -chr10 123276854 123276857 FGFR2(NM_000141.4):codon_S354 -chr10 123274801 123274804 FGFR2(NM_000141.4):codon_S372 -chr10 123274792 123274795 FGFR2(NM_000141.4):codon_Y375 -chr10 123274771 123274774 FGFR2(NM_000141.4):codon_C382 -chr10 123274744 123274747 FGFR2(NM_000141.4):codon_M391 -chr10 123274732 123274735 FGFR2(NM_000141.4):codon_V395 -chr10 123258069 123258072 FGFR2(NM_000141.4):codon_M537 -chr10 123258039 123258042 FGFR2(NM_000141.4):codon_I547 -chr10 123258033 123258036 FGFR2(NM_000141.4):codon_N549 -chr10 123256216 123256219 FGFR2(NM_000141.4):codon_V564 -chr10 123256213 123256216 FGFR2(NM_000141.4):codon_E565 -chr10 123256201 123256204 FGFR2(NM_000141.4):codon_K569 -chr10 123256057 123256060 FGFR2(NM_000141.4):codon_L617 -chr10 123247582 123247585 FGFR2(NM_000141.4):codon_E636 -chr10 123247567 123247570 FGFR2(NM_000141.4):codon_K641 -chr10 123247513 123247516 FGFR2(NM_000141.4):codon_K659 -chr10 123246932 123246935 FGFR2(NM_000141.4):codon_R664 -chr10 123246890 123246893 FGFR2(NM_000141.4):codon_R678 diff --git a/hotspot_coverage/fight-209_combined.groups b/hotspot_coverage/fight-209_combined.groups deleted file mode 100644 index e9a7d0e..0000000 --- a/hotspot_coverage/fight-209_combined.groups +++ /dev/null @@ -1,50 +0,0 @@ -GENE -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR1 -FGFR1 -FGFR1 -FGFR1 -FGFR1 -FGFR1 -FGFR1 -FGFR1 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 diff --git a/hotspot_coverage/fight-209_hotspots.bed b/hotspot_coverage/fight-209_hotspots.bed deleted file mode 100644 index 3c1b78a..0000000 --- a/hotspot_coverage/fight-209_hotspots.bed +++ /dev/null @@ -1,57 +0,0 @@ -chr4 1803245 1803248 FGFR3(NM_000142.4):codon_R200 -chr4 1803563 1803566 FGFR3(NM_000142.4):codon_R248 -chr4 1803566 1803569 FGFR3(NM_000142.4):codon_S249 -chr4 1805511 1805514 FGFR3(NM_000142.4):codon_G342 -chr4 1806056 1806247 FGFR3(NM_000142.4):exon_9 -chr4 1806088 1806091 FGFR3(NM_000142.4):codon_G370 -chr4 1806091 1806094 FGFR3(NM_000142.4):codon_S371 -chr4 1806097 1806100 FGFR3(NM_000142.4):codon_Y373 -chr4 1806103 1806106 FGFR3(NM_000142.4):codon_G375 -chr4 1806118 1806121 FGFR3(NM_000142.4):codon_G380 -chr4 1806151 1806154 FGFR3(NM_000142.4):codon_A391 -chr4 1807332 1807335 FGFR3(NM_000142.4):codon_M528 -chr4 1807368 1807371 FGFR3(NM_000142.4):codon_N540 -chr4 1807493 1807496 FGFR3(NM_000142.4):codon_V555 -chr4 1807801 1807804 FGFR3(NM_000142.4):codon_R621 -chr4 1807861 1807864 FGFR3(NM_000142.4):codon_D641 -chr4 1807888 1807891 FGFR3(NM_000142.4):codon_K650 -chr8 38285492 38285495 FGFR1(NM_023110.2):codon_R189 -chr8 38282206 38282209 FGFR1(NM_023110.2):codon_P252 -chr8 38277212 38277215 FGFR1(NM_023110.2):codon_Y374 -chr8 38277191 38277194 FGFR1(NM_023110.2):codon_C381 -chr8 38275840 38275843 FGFR1(NM_023110.2):codon_R445 -chr8 38274848 38274851 FGFR1(NM_023110.2):codon_N546 -chr8 38273558 38273561 FGFR1(NM_023110.2):codon_V561 -chr8 38272305 38272308 FGFR1(NM_023110.2):codon_K656 -chr10 123310899 123310929 FGFR2(NM_000141.4):exon_5_partial_p167-176 -chr10 123310818 123310821 FGFR2(NM_000141.4):codon_R203 -chr10 123298223 123298226 FGFR2(NM_000141.4):codon_R210 -chr10 123279675 123279678 FGFR2(NM_000141.4):codon_S252 -chr10 123279672 123279675 FGFR2(NM_000141.4):codon_P253 -chr10 123279612 123279666 FGFR2(NM_000141.4):exon_7_partial_p256-273 -chr10 123279630 123279633 FGFR2(NM_000141.4):codon_S267 -chr10 123279561 123279564 FGFR2(NM_000141.4):codon_W290 -chr10 123279495 123279594 FGFR2(NM_000141.4):exon_7_partial_p280-312 -chr10 123276971 123276974 FGFR2(NM_000141.4):codon_A315 -chr10 123276908 123276911 FGFR2(NM_000141.4):codon_D336 -chr10 123276890 123276893 FGFR2(NM_000141.4):codon_C342 -chr10 123276875 123276878 FGFR2(NM_000141.4):codon_S347 -chr10 123276863 123276866 FGFR2(NM_000141.4):codon_S351 -chr10 123276854 123276857 FGFR2(NM_000141.4):codon_S354 -chr10 123274801 123274804 FGFR2(NM_000141.4):codon_S372 -chr10 123274792 123274795 FGFR2(NM_000141.4):codon_Y375 -chr10 123274771 123274774 FGFR2(NM_000141.4):codon_C382 -chr10 123274744 123274747 FGFR2(NM_000141.4):codon_M391 -chr10 123274732 123274735 FGFR2(NM_000141.4):codon_V395 -chr10 123258069 123258072 FGFR2(NM_000141.4):codon_M537 -chr10 123258039 123258042 FGFR2(NM_000141.4):codon_I547 -chr10 123258033 123258036 FGFR2(NM_000141.4):codon_N549 -chr10 123256216 123256219 FGFR2(NM_000141.4):codon_V564 -chr10 123256213 123256216 FGFR2(NM_000141.4):codon_E565 -chr10 123256201 123256204 FGFR2(NM_000141.4):codon_K569 -chr10 123256057 123256060 FGFR2(NM_000141.4):codon_L617 -chr10 123247582 123247585 FGFR2(NM_000141.4):codon_E636 -chr10 123247567 123247570 FGFR2(NM_000141.4):codon_K641 -chr10 123247513 123247516 FGFR2(NM_000141.4):codon_K659 -chr10 123246932 123246935 FGFR2(NM_000141.4):codon_R664 -chr10 123246890 123246893 FGFR2(NM_000141.4):codon_R678 diff --git a/hotspot_coverage/fight-209_hotspots.groups b/hotspot_coverage/fight-209_hotspots.groups deleted file mode 100644 index f62ee1b..0000000 --- a/hotspot_coverage/fight-209_hotspots.groups +++ /dev/null @@ -1,58 +0,0 @@ -GENE -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR3 -FGFR1 -FGFR1 -FGFR1 -FGFR1 -FGFR1 -FGFR1 -FGFR1 -FGFR1 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 -FGFR2 diff --git a/hotspot_coverage/mpn_combined.bed b/hotspot_coverage/mpn_combined.bed deleted file mode 100644 index a18c916..0000000 --- a/hotspot_coverage/mpn_combined.bed +++ /dev/null @@ -1,4 +0,0 @@ -chr1 43814928 43815035 MPL(NM_005373.2):exon_10 -chr9 5069919 5070057 JAK2(NM_004972.3):exon_12 -chr9 5073763 5073778 JAK2(NM_004972.3):codon_V617 -chr19 13054521 13054732 CALR(NM_004343.3):exon_9 diff --git a/hotspot_coverage/mpn_combined.groups b/hotspot_coverage/mpn_combined.groups deleted file mode 100644 index ae0cf0a..0000000 --- a/hotspot_coverage/mpn_combined.groups +++ /dev/null @@ -1,5 +0,0 @@ -GENE -MPL -JAK2 -JAK2 -CALR diff --git a/hotspot_coverage/mpn_genescreen.bed b/hotspot_coverage/mpn_genescreen.bed deleted file mode 100644 index a18c916..0000000 --- a/hotspot_coverage/mpn_genescreen.bed +++ /dev/null @@ -1,4 +0,0 @@ -chr1 43814928 43815035 MPL(NM_005373.2):exon_10 -chr9 5069919 5070057 JAK2(NM_004972.3):exon_12 -chr9 5073763 5073778 JAK2(NM_004972.3):codon_V617 -chr19 13054521 13054732 CALR(NM_004343.3):exon_9 diff --git a/hotspot_coverage/mpn_genescreen.groups b/hotspot_coverage/mpn_genescreen.groups deleted file mode 100644 index ae0cf0a..0000000 --- a/hotspot_coverage/mpn_genescreen.groups +++ /dev/null @@ -1,5 +0,0 @@ -GENE -MPL -JAK2 -JAK2 -CALR diff --git a/hotspot_coverage/myeloid_combined.bed b/hotspot_coverage/myeloid_combined.bed deleted file mode 100644 index ca58ea9..0000000 --- a/hotspot_coverage/myeloid_combined.bed +++ /dev/null @@ -1,132 +0,0 @@ -chr1 43814928 43815035 MPL(NM_005373.2):exon_10 -chr1 115256521 115256536 NRAS(NM_002524.4):codon_Q61 -chr1 115258736 115258754 NRAS(NM_002524.4):codons_G12-13 -chr2 25457142 25457294 DNMT3A(NM_175629.2):exon_23 -chr2 25458570 25458699 DNMT3A(NM_175629.2):exon_22 -chr2 25459799 25459879 DNMT3A(NM_175629.2):exon_21 -chr2 25461993 25462089 DNMT3A(NM_175629.2):exon_20 -chr2 25463165 25463324 DNMT3A(NM_175629.2):exon_19 -chr2 25463503 25463604 DNMT3A(NM_175629.2):exon_18 -chr2 25464425 25464581 DNMT3A(NM_175629.2):exon_17 -chr2 25466761 25466856 DNMT3A(NM_175629.2):exon_16 -chr2 25467018 25467212 DNMT3A(NM_175629.2):exon_15 -chr2 25467403 25467526 DNMT3A(NM_175629.2):exon_14 -chr2 25468116 25468206 DNMT3A(NM_175629.2):exon_13 -chr2 25468883 25468938 DNMT3A(NM_175629.2):exon_12 -chr2 25469023 25469183 DNMT3A(NM_175629.2):exon_11 -chr2 25469483 25469650 DNMT3A(NM_175629.2):exon_10 -chr2 25469914 25470032 DNMT3A(NM_175629.2):exon_9 -chr2 25470454 25470623 DNMT3A(NM_175629.2):exon_8 -chr2 25470900 25471126 DNMT3A(NM_175629.2):exon_7 -chr2 25472520 25472598 DNMT3A(NM_153759.3):exon_2 -chr2 25475057 25475071 DNMT3A(NM_153759.3):exon_1 -chr2 25497804 25497961 DNMT3A(NM_175629.2):exon_6 -chr2 25498363 25498417 DNMT3A(NM_175629.2):exon_5 -chr2 25505304 25505585 DNMT3A(NM_175629.2):exon_4 -chr2 25523002 25523117 DNMT3A(NM_175629.2):exon_3 -chr2 25536776 25536858 DNMT3A(NM_175629.2):exon_2 -chr2 198266460 198266617 SF3B1(NM_012433.3):exon_16 -chr2 198266703 198266859 SF3B1(NM_012433.3):exon_15 -chr2 198267274 198267555 SF3B1(NM_012433.3):exon_14 -chr2 198267667 198267764 SF3B1(NM_012433.3):exon_13 -chr2 209113104 209113119 IDH1(NM_005896.3):codon_R132 -chr3 128199856 128200166 GATA2(NM_032638.4):exon_6 -chr3 128200656 128200792 GATA2(NM_032638.4):exon_5 -chr3 128202697 128202853 GATA2(NM_032638.4):exon_4 -chr3 128204564 128205216 GATA2(NM_032638.4):exon_3 -chr3 128205640 128205879 GATA2(NM_032638.4):exon_2 -chr4 55141002 55141145 PDGFRA(NM_006206.5):exon_12 -chr4 55144057 55144178 PDGFRA(NM_006206.5):exon_14 -chr4 55152002 55152135 PDGFRA(NM_006206.5):exon_18 -chr4 55152100 55152115 PDGFRA(NM_006206.5):codon_S847 -chr4 55599230 55599363 KIT(NM_000222.2):exon_17 -chr4 106155094 106158602 TET2(NM_001127208.2):exon_3 -chr4 106162490 106162591 TET2(NM_001127208.2):exon_4 -chr4 106163985 106164089 TET2(NM_001127208.2):exon_5 -chr4 106164721 106164940 TET2(NM_001127208.2):exon_6 -chr4 106180770 106180931 TET2(NM_001127208.2):exon_7 -chr4 106182910 106183010 TET2(NM_001127208.2):exon_8 -chr4 106190761 106190909 TET2(NM_001127208.2):exon_9 -chr4 106193715 106194080 TET2(NM_001127208.2):exon_10 -chr4 106196199 106197681 TET2(NM_001127208.2):exon_11 -chr5 170837525 170837574 NPM1(NM_002520.6):exon_11 -chr7 148504732 148504803 EZH2(NM_004456.4):exon_20 -chr7 148506157 148506252 EZH2(NM_004456.4):exon_19 -chr7 148506396 148506487 EZH2(NM_004456.4):exon_18 -chr7 148507419 148507511 EZH2(NM_004456.4):exon_17 -chr7 148508711 148508817 EZH2(NM_004456.4):exon_16 -chr7 148508719 148508734 EZH2(NM_004456.4):codon_Y646 -chr7 148511045 148511234 EZH2(NM_004456.4):exon_15 -chr7 148512000 148512136 EZH2(NM_004456.4):exon_14 -chr7 148512592 148512643 EZH2(NM_004456.4):exon_13 -chr7 148513770 148513875 EZH2(NM_004456.4):exon_12 -chr7 148514308 148514488 EZH2(NM_004456.4):exon_11 -chr7 148514963 148515214 EZH2(NM_004456.4):exon_10 -chr7 148516682 148516784 EZH2(NM_004456.4):exon_9 -chr7 148523540 148523729 EZH2(NM_004456.4):exon_8 -chr7 148524250 148524363 EZH2(NM_004456.4):exon_7 -chr7 148525826 148525977 EZH2(NM_004456.4):exon_6 -chr7 148526814 148526945 EZH2(NM_004456.4):exon_5 -chr7 148529720 148529847 EZH2(NM_004456.4):exon_4 -chr7 148543556 148543695 EZH2(NM_004456.4):exon_3 -chr7 148544268 148544395 EZH2(NM_004456.4):exon_2 -chr9 5069919 5070057 JAK2(NM_004972.3):exon_12 -chr9 5073763 5073778 JAK2(NM_004972.3):codon_V617 -chr9 139390517 139392015 NOTCH1(NM_017617.4):exon_34 -chr11 119148870 119149012 CBL(NM_005188.3):exon_8 -chr11 119149214 119149428 CBL(NM_005188.3):exon_9 -chr12 11803056 11803099 ETV6(NM_001987.4):exon_1 -chr12 11905378 11905518 ETV6(NM_001987.4):exon_2 -chr12 11992068 11992243 ETV6(NM_001987.4):exon_3 -chr12 12006355 12006500 ETV6(NM_001987.4):exon_4 -chr12 12022352 12022908 ETV6(NM_001987.4):exon_5 -chr12 12037373 12037526 ETV6(NM_001987.4):exon_6 -chr12 12038854 12038965 ETV6(NM_001987.4):exon_7 -chr12 12043869 12043985 ETV6(NM_001987.4):exon_8 -chr12 25380162 25380351 KRAS(NM_033360.3):exon_3 -chr12 25398202 25398323 KRAS(NM_033360.3):exon_2 -chr13 28592598 28592731 FLT3(NM_004119.2):exon_20 -chr13 28608018 28608133 FLT3(NM_004119.2):exon_15 -chr13 28608213 28608356 FLT3(NM_004119.2):exon_14 -chr13 28608432 28608549 FLT3(NM_004119.2):exon_13 -chr15 90631813 90631984 IDH2(NM_002168.3):exon_4 -chr17 7572921 7573013 TP53(NM_000546.5):exon_11 -chr17 7573921 7574038 TP53(NM_000546.5):exon_10 -chr17 7576847 7576931 TP53(NM_000546.5):exon_9 -chr17 7577013 7577160 TP53(NM_000546.5):exon_8 -chr17 7577493 7577613 TP53(NM_000546.5):exon_7 -chr17 7578171 7578294 TP53(NM_000546.5):exon_6 -chr17 7578365 7578559 TP53(NM_000546.5):exon_5 -chr17 7579306 7579595 TP53(NM_000546.5):exon_4 -chr17 7579694 7579726 TP53(NM_000546.5):exon_3 -chr17 7579833 7579917 TP53(NM_000546.5):exon_2 -chr17 74732875 74733247 SRSF2(NM_003016.4):exon_1 -chr18 42531876 42532065 SETBP1(NM_015559.2):exon_4_(partial) -chr19 13054521 13054732 CALR(NM_004343.3):exon_9 -chr19 33792238 33793325 CEBPA(NM_004364.4):exon_1 -chr20 31022229 31025146 ASXL1(NM_015338.5):exon_13 -chr21 36164426 36164912 RUNX1(NM_001754.4):exon_9 -chr21 36171592 36171764 RUNX1(NM_001754.4):exon_8 -chr21 36193959 36193998 RUNX1(NM_001122607.1):exon_5 -chr21 36206701 36206903 RUNX1(NM_001754.4):exon_7 -chr21 36231765 36231880 RUNX1(NM_001754.4):exon_6 -chr21 36252848 36253015 RUNX1(NM_001754.4):exon_5 -chr21 36259134 36259414 RUNX1(NM_001754.4):exon_4 -chr21 36265216 36265265 RUNX1(NM_001754.4):exon_3 -chr21 36421133 36421201 RUNX1(NM_001754.4):exon_2 -chr21 44514769 44514784 U2AF1(NM_006758.2):codon_Q157 -chr21 44524448 44524463 U2AF1(NM_006758.2):codon_S34 -chrX 39911356 39911658 BCOR(NM_001123385.1):exon_15 -chrX 39913133 39913300 BCOR(NM_001123385.1):exon_14 -chrX 39913503 39913591 BCOR(NM_001123385.1):exon_13 -chrX 39914615 39914771 BCOR(NM_001123385.1):exon_12 -chrX 39916402 39916579 BCOR(NM_001123385.1):exon_11 -chrX 39921386 39921651 BCOR(NM_001123385.1):exon_10 -chrX 39921993 39922329 BCOR(NM_001123385.1):exon_9 -chrX 39922855 39923210 BCOR(NM_001123385.1):exon_8 -chrX 39923583 39923857 BCOR(NM_001123385.1):exon_7 -chrX 39930220 39930417 BCOR(NM_001123385.1):exon_6 -chrX 39930884 39930948 BCOR(NM_001123385.1):exon_5 -chrX 39931596 39934438 BCOR(NM_001123385.1):exon_4 -chrX 39935701 39935790 BCOR(NM_001123385.1):exon_3 -chrX 39937091 39937187 BCOR(NM_001123385.1):exon_2 diff --git a/hotspot_coverage/myeloid_combined.groups b/hotspot_coverage/myeloid_combined.groups deleted file mode 100644 index 1743edf..0000000 --- a/hotspot_coverage/myeloid_combined.groups +++ /dev/null @@ -1,133 +0,0 @@ -GENE -MPL -NRAS -NRAS -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -SF3B1 -SF3B1 -SF3B1 -SF3B1 -IDH1 -GATA2 -GATA2 -GATA2 -GATA2 -GATA2 -PDGFRA -PDGFRA -PDGFRA -PDGFRA -KIT -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -NPM1 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -JAK2 -JAK2 -NOTCH1 -CBL -CBL -ETV6 -ETV6 -ETV6 -ETV6 -ETV6 -ETV6 -ETV6 -ETV6 -KRAS -KRAS -FLT3 -FLT3 -FLT3 -FLT3 -IDH2 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -SRSF2 -SETBP1 -CALR -CEBPA -ASXL1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -U2AF1 -U2AF1 -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR diff --git a/hotspot_coverage/myeloid_genescreen.bed b/hotspot_coverage/myeloid_genescreen.bed deleted file mode 100644 index ca58ea9..0000000 --- a/hotspot_coverage/myeloid_genescreen.bed +++ /dev/null @@ -1,132 +0,0 @@ -chr1 43814928 43815035 MPL(NM_005373.2):exon_10 -chr1 115256521 115256536 NRAS(NM_002524.4):codon_Q61 -chr1 115258736 115258754 NRAS(NM_002524.4):codons_G12-13 -chr2 25457142 25457294 DNMT3A(NM_175629.2):exon_23 -chr2 25458570 25458699 DNMT3A(NM_175629.2):exon_22 -chr2 25459799 25459879 DNMT3A(NM_175629.2):exon_21 -chr2 25461993 25462089 DNMT3A(NM_175629.2):exon_20 -chr2 25463165 25463324 DNMT3A(NM_175629.2):exon_19 -chr2 25463503 25463604 DNMT3A(NM_175629.2):exon_18 -chr2 25464425 25464581 DNMT3A(NM_175629.2):exon_17 -chr2 25466761 25466856 DNMT3A(NM_175629.2):exon_16 -chr2 25467018 25467212 DNMT3A(NM_175629.2):exon_15 -chr2 25467403 25467526 DNMT3A(NM_175629.2):exon_14 -chr2 25468116 25468206 DNMT3A(NM_175629.2):exon_13 -chr2 25468883 25468938 DNMT3A(NM_175629.2):exon_12 -chr2 25469023 25469183 DNMT3A(NM_175629.2):exon_11 -chr2 25469483 25469650 DNMT3A(NM_175629.2):exon_10 -chr2 25469914 25470032 DNMT3A(NM_175629.2):exon_9 -chr2 25470454 25470623 DNMT3A(NM_175629.2):exon_8 -chr2 25470900 25471126 DNMT3A(NM_175629.2):exon_7 -chr2 25472520 25472598 DNMT3A(NM_153759.3):exon_2 -chr2 25475057 25475071 DNMT3A(NM_153759.3):exon_1 -chr2 25497804 25497961 DNMT3A(NM_175629.2):exon_6 -chr2 25498363 25498417 DNMT3A(NM_175629.2):exon_5 -chr2 25505304 25505585 DNMT3A(NM_175629.2):exon_4 -chr2 25523002 25523117 DNMT3A(NM_175629.2):exon_3 -chr2 25536776 25536858 DNMT3A(NM_175629.2):exon_2 -chr2 198266460 198266617 SF3B1(NM_012433.3):exon_16 -chr2 198266703 198266859 SF3B1(NM_012433.3):exon_15 -chr2 198267274 198267555 SF3B1(NM_012433.3):exon_14 -chr2 198267667 198267764 SF3B1(NM_012433.3):exon_13 -chr2 209113104 209113119 IDH1(NM_005896.3):codon_R132 -chr3 128199856 128200166 GATA2(NM_032638.4):exon_6 -chr3 128200656 128200792 GATA2(NM_032638.4):exon_5 -chr3 128202697 128202853 GATA2(NM_032638.4):exon_4 -chr3 128204564 128205216 GATA2(NM_032638.4):exon_3 -chr3 128205640 128205879 GATA2(NM_032638.4):exon_2 -chr4 55141002 55141145 PDGFRA(NM_006206.5):exon_12 -chr4 55144057 55144178 PDGFRA(NM_006206.5):exon_14 -chr4 55152002 55152135 PDGFRA(NM_006206.5):exon_18 -chr4 55152100 55152115 PDGFRA(NM_006206.5):codon_S847 -chr4 55599230 55599363 KIT(NM_000222.2):exon_17 -chr4 106155094 106158602 TET2(NM_001127208.2):exon_3 -chr4 106162490 106162591 TET2(NM_001127208.2):exon_4 -chr4 106163985 106164089 TET2(NM_001127208.2):exon_5 -chr4 106164721 106164940 TET2(NM_001127208.2):exon_6 -chr4 106180770 106180931 TET2(NM_001127208.2):exon_7 -chr4 106182910 106183010 TET2(NM_001127208.2):exon_8 -chr4 106190761 106190909 TET2(NM_001127208.2):exon_9 -chr4 106193715 106194080 TET2(NM_001127208.2):exon_10 -chr4 106196199 106197681 TET2(NM_001127208.2):exon_11 -chr5 170837525 170837574 NPM1(NM_002520.6):exon_11 -chr7 148504732 148504803 EZH2(NM_004456.4):exon_20 -chr7 148506157 148506252 EZH2(NM_004456.4):exon_19 -chr7 148506396 148506487 EZH2(NM_004456.4):exon_18 -chr7 148507419 148507511 EZH2(NM_004456.4):exon_17 -chr7 148508711 148508817 EZH2(NM_004456.4):exon_16 -chr7 148508719 148508734 EZH2(NM_004456.4):codon_Y646 -chr7 148511045 148511234 EZH2(NM_004456.4):exon_15 -chr7 148512000 148512136 EZH2(NM_004456.4):exon_14 -chr7 148512592 148512643 EZH2(NM_004456.4):exon_13 -chr7 148513770 148513875 EZH2(NM_004456.4):exon_12 -chr7 148514308 148514488 EZH2(NM_004456.4):exon_11 -chr7 148514963 148515214 EZH2(NM_004456.4):exon_10 -chr7 148516682 148516784 EZH2(NM_004456.4):exon_9 -chr7 148523540 148523729 EZH2(NM_004456.4):exon_8 -chr7 148524250 148524363 EZH2(NM_004456.4):exon_7 -chr7 148525826 148525977 EZH2(NM_004456.4):exon_6 -chr7 148526814 148526945 EZH2(NM_004456.4):exon_5 -chr7 148529720 148529847 EZH2(NM_004456.4):exon_4 -chr7 148543556 148543695 EZH2(NM_004456.4):exon_3 -chr7 148544268 148544395 EZH2(NM_004456.4):exon_2 -chr9 5069919 5070057 JAK2(NM_004972.3):exon_12 -chr9 5073763 5073778 JAK2(NM_004972.3):codon_V617 -chr9 139390517 139392015 NOTCH1(NM_017617.4):exon_34 -chr11 119148870 119149012 CBL(NM_005188.3):exon_8 -chr11 119149214 119149428 CBL(NM_005188.3):exon_9 -chr12 11803056 11803099 ETV6(NM_001987.4):exon_1 -chr12 11905378 11905518 ETV6(NM_001987.4):exon_2 -chr12 11992068 11992243 ETV6(NM_001987.4):exon_3 -chr12 12006355 12006500 ETV6(NM_001987.4):exon_4 -chr12 12022352 12022908 ETV6(NM_001987.4):exon_5 -chr12 12037373 12037526 ETV6(NM_001987.4):exon_6 -chr12 12038854 12038965 ETV6(NM_001987.4):exon_7 -chr12 12043869 12043985 ETV6(NM_001987.4):exon_8 -chr12 25380162 25380351 KRAS(NM_033360.3):exon_3 -chr12 25398202 25398323 KRAS(NM_033360.3):exon_2 -chr13 28592598 28592731 FLT3(NM_004119.2):exon_20 -chr13 28608018 28608133 FLT3(NM_004119.2):exon_15 -chr13 28608213 28608356 FLT3(NM_004119.2):exon_14 -chr13 28608432 28608549 FLT3(NM_004119.2):exon_13 -chr15 90631813 90631984 IDH2(NM_002168.3):exon_4 -chr17 7572921 7573013 TP53(NM_000546.5):exon_11 -chr17 7573921 7574038 TP53(NM_000546.5):exon_10 -chr17 7576847 7576931 TP53(NM_000546.5):exon_9 -chr17 7577013 7577160 TP53(NM_000546.5):exon_8 -chr17 7577493 7577613 TP53(NM_000546.5):exon_7 -chr17 7578171 7578294 TP53(NM_000546.5):exon_6 -chr17 7578365 7578559 TP53(NM_000546.5):exon_5 -chr17 7579306 7579595 TP53(NM_000546.5):exon_4 -chr17 7579694 7579726 TP53(NM_000546.5):exon_3 -chr17 7579833 7579917 TP53(NM_000546.5):exon_2 -chr17 74732875 74733247 SRSF2(NM_003016.4):exon_1 -chr18 42531876 42532065 SETBP1(NM_015559.2):exon_4_(partial) -chr19 13054521 13054732 CALR(NM_004343.3):exon_9 -chr19 33792238 33793325 CEBPA(NM_004364.4):exon_1 -chr20 31022229 31025146 ASXL1(NM_015338.5):exon_13 -chr21 36164426 36164912 RUNX1(NM_001754.4):exon_9 -chr21 36171592 36171764 RUNX1(NM_001754.4):exon_8 -chr21 36193959 36193998 RUNX1(NM_001122607.1):exon_5 -chr21 36206701 36206903 RUNX1(NM_001754.4):exon_7 -chr21 36231765 36231880 RUNX1(NM_001754.4):exon_6 -chr21 36252848 36253015 RUNX1(NM_001754.4):exon_5 -chr21 36259134 36259414 RUNX1(NM_001754.4):exon_4 -chr21 36265216 36265265 RUNX1(NM_001754.4):exon_3 -chr21 36421133 36421201 RUNX1(NM_001754.4):exon_2 -chr21 44514769 44514784 U2AF1(NM_006758.2):codon_Q157 -chr21 44524448 44524463 U2AF1(NM_006758.2):codon_S34 -chrX 39911356 39911658 BCOR(NM_001123385.1):exon_15 -chrX 39913133 39913300 BCOR(NM_001123385.1):exon_14 -chrX 39913503 39913591 BCOR(NM_001123385.1):exon_13 -chrX 39914615 39914771 BCOR(NM_001123385.1):exon_12 -chrX 39916402 39916579 BCOR(NM_001123385.1):exon_11 -chrX 39921386 39921651 BCOR(NM_001123385.1):exon_10 -chrX 39921993 39922329 BCOR(NM_001123385.1):exon_9 -chrX 39922855 39923210 BCOR(NM_001123385.1):exon_8 -chrX 39923583 39923857 BCOR(NM_001123385.1):exon_7 -chrX 39930220 39930417 BCOR(NM_001123385.1):exon_6 -chrX 39930884 39930948 BCOR(NM_001123385.1):exon_5 -chrX 39931596 39934438 BCOR(NM_001123385.1):exon_4 -chrX 39935701 39935790 BCOR(NM_001123385.1):exon_3 -chrX 39937091 39937187 BCOR(NM_001123385.1):exon_2 diff --git a/hotspot_coverage/myeloid_genescreen.groups b/hotspot_coverage/myeloid_genescreen.groups deleted file mode 100644 index 1743edf..0000000 --- a/hotspot_coverage/myeloid_genescreen.groups +++ /dev/null @@ -1,133 +0,0 @@ -GENE -MPL -NRAS -NRAS -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -DNMT3A -SF3B1 -SF3B1 -SF3B1 -SF3B1 -IDH1 -GATA2 -GATA2 -GATA2 -GATA2 -GATA2 -PDGFRA -PDGFRA -PDGFRA -PDGFRA -KIT -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -TET2 -NPM1 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -EZH2 -JAK2 -JAK2 -NOTCH1 -CBL -CBL -ETV6 -ETV6 -ETV6 -ETV6 -ETV6 -ETV6 -ETV6 -ETV6 -KRAS -KRAS -FLT3 -FLT3 -FLT3 -FLT3 -IDH2 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -TP53 -SRSF2 -SETBP1 -CALR -CEBPA -ASXL1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -RUNX1 -U2AF1 -U2AF1 -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR -BCOR diff --git a/hotspot_variants/Colorectal.bed b/hotspot_variants/Colorectal.bed deleted file mode 100644 index e6ccc70..0000000 --- a/hotspot_variants/Colorectal.bed +++ /dev/null @@ -1,34 +0,0 @@ -1 115252184 115252354 NRAS(NM_002524.3):c.450+6_c.291-5 -1 115256415 115256604 NRAS(NM_002524.3):c.290+6_c.112-5 -1 115258665 115258786 NRAS(NM_002524.3):c.111+6_c.-5 -3 178935992 178936127 PIK3CA(NM_006218.2):c.1540-5_1664+5 -3 178951876 178952157 PIK3CA(NM_006218.2):c.2937-5_*5 -7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 -10 89624221 89624310 PTEN(NM_000314.4):c.-6_79+5 -10 89653776 89653871 PTEN(NM_000314.4):c.80-5_164+5 -10 89685264 89685319 PTEN(NM_000314.4):c.165-5_209+5 -10 89690797 89690851 PTEN(NM_000314.4):c.210-5_253+5 -10 89692764 89693013 PTEN(NM_000314.4):c.254-5_492+5 -10 89711869 89712021 PTEN(NM_000314.4):c.493-5_634+5 -10 89717604 89717781 PTEN(NM_000314.4):c.635-5_801+5 -10 89720645 89720880 PTEN(NM_000314.4):c.802-5_1026+5 -10 89725038 89725234 PTEN(NM_000314.4):c.1027-5_*5 -12 25378542 25378712 KRAS(NM_004985.3):c.450+6_c.291-5 -12 25380162 25380351 KRAS(NM_004985.3):c.290+6_c.112-5 -12 25398202 25398323 KRAS(NM_004985.3):c.111+6_c.-5 -17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5 -17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5 -17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T -17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5 -17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5 -17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5 -17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5 -17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5 -17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5 -17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5 -17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5 diff --git a/hotspot_variants/GIST.bed b/hotspot_variants/GIST.bed deleted file mode 100644 index c5f06a1..0000000 --- a/hotspot_variants/GIST.bed +++ /dev/null @@ -1,8 +0,0 @@ -4 55141002 55141145 PDGFRA(NM_006206.4):c.1654-5_1786+5 -4 55144057 55144178 PDGFRA(NM_006206.4):c.1892-5_2002+5 -4 55152002 55152135 PDGFRA(NM_006206.4):c.2440-5_2562+5 -4 55592017 55592221 KIT(NM_000222.2):c.1347-5_1540+5 -4 55593576 55593713 KIT(NM_000222.2):c.1648-5_1774+5 -4 55594171 55594292 KIT(NM_000222.2):c.1880-5_1990+5 -4 55595495 55595656 KIT(NM_000222.2):c.1991-5_2141+5 -4 55599230 55599363 KIT(NM_000222.2):c.2362-5_2484+5 diff --git a/hotspot_variants/Glioma.bed b/hotspot_variants/Glioma.bed deleted file mode 100644 index b54e4ea..0000000 --- a/hotspot_variants/Glioma.bed +++ /dev/null @@ -1,68 +0,0 @@ -1 226252024 226252185 H3F3A(NM_002107.4):c.-23-6_128+5 -2 209113087 209113389 IDH1(NM_005896.2):c.414+6_c.123-5 -5 1295227 1295228 TERT(NM_198253.2):c.-124_-124 -5 1295249 1295250 TERT(NM_198253.2):c.-146_-146 -7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -9 21968222 21968246 CDKN2A(NM_000077.3):c.*6_458-5 -9 21970895 21971212 CDKN2A(NM_000077.3):c.151-5_457+5 -9 21974671 21974831 CDKN2A(NM_000077.3):c.150+5_-5 -10 89624221 89624310 PTEN(NM_000314.4):c.-6_79+5 -10 89653776 89653871 PTEN(NM_000314.4):c.80-5_164+5 -10 89685264 89685319 PTEN(NM_000314.4):c.165-5_209+5 -10 89690797 89690851 PTEN(NM_000314.4):c.210-5_253+5 -10 89692764 89693013 PTEN(NM_000314.4):c.254-5_492+5 -10 89711869 89712021 PTEN(NM_000314.4):c.493-5_634+5 -10 89717604 89717781 PTEN(NM_000314.4):c.635-5_801+5 -10 89720645 89720880 PTEN(NM_000314.4):c.802-5_1026+5 -10 89725038 89725234 PTEN(NM_000314.4):c.1027-5_*5 -15 90631813 90631984 IDH2(NM_002168.2):c.534+6_c.374-5 -17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5 -17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5 -17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T -17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5 -17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5 -17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5 -17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5 -17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5 -17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5 -17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5 -17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5 -X 76763824 76764113 ATRX(NM_000489.3):c.7201-6_c*5 -X 76776260 76776399 ATRX(NM_000489.3):c.7072-5_7200+5 -X 76776875 76776981 ATRX(NM_000489.3):c.6976-5_7071+5 -X 76777735 76777871 ATRX(NM_000489.3):c.6850-5_6975+5 -X 76778724 76778884 ATRX(NM_000489.3):c.6700-5_6849+5 -X 76812916 76813121 ATRX(NM_000489.3):c.6505-5_6699+5 -X 76814134 76814322 ATRX(NM_000489.3):c.6327-5_6504+5 -X 76829709 76829828 ATRX(NM_000489.3):c.6218-5_6326+5 -X 76845298 76845415 ATRX(NM_000489.3):c.6111-5_6217+5 -X 76849160 76849324 ATRX(NM_000489.3):c.5957-5_6110+5 -X 76854874 76855054 ATRX(NM_000489.3):c.5787-5_5956+5 -X 76855195 76855294 ATRX(NM_000489.3):c.5698-5_5786+5 -X 76855897 76856038 ATRX(NM_000489.3):c.5567-5_5697+5 -X 76872075 76872203 ATRX(NM_000489.3):c.5449-5_5566+5 -X 76874268 76874454 ATRX(NM_000489.3):c.5273-5_5448+5 -X 76875857 76876005 ATRX(NM_000489.3):c.5135-5_5272+5 -X 76888689 76888877 ATRX(NM_000489.3):c.4957-5_5134+5 -X 76889048 76889205 ATRX(NM_000489.3):c.4810-5_4956+5 -X 76890079 76890199 ATRX(NM_000489.3):c.4700-5_4809+5 -X 76891400 76891552 ATRX(NM_000489.3):c.4558-5_4699+5 -X 76907598 76907848 ATRX(NM_000489.3):c.4318-5_4557+5 -X 76909582 76909695 ATRX(NM_000489.3):c.4215-5_4317+5 -X 76912044 76912148 ATRX(NM_000489.3):c.4121-5_4214+5 -X 76918865 76919052 ATRX(NM_000489.3):c.3944-5_4120+5 -X 76920128 76920272 ATRX(NM_000489.3):c.3810-5_3943+5 -X 76931715 76931798 ATRX(NM_000489.3):c.3737-5_3809+5 -X 76937006 76940090 ATRX(NM_000489.3):c.663-5_3736+5 -X 76940425 76940503 ATRX(NM_000489.3):c.595-5_662+5 -X 76944305 76944425 ATRX(NM_000489.3):c.485-5_594+5 -X 76949307 76949431 ATRX(NM_000489.3):c.371-5_484+5 -X 76952059 76952197 ATRX(NM_000489.3):c.243-5_370+5 -X 76953065 76953128 ATRX(NM_000489.3):c.190-5_242+5 -X 76954056 76954122 ATRX(NM_000489.3):c.134-5_189+5 -X 76972602 76972725 ATRX(NM_000489.3):c.21-5_133+5 -X 77041462 77041492 ATRX(NM_000489.3):c.-5_20+5 diff --git a/hotspot_variants/Lung.bed b/hotspot_variants/Lung.bed deleted file mode 100644 index a9499c9..0000000 --- a/hotspot_variants/Lung.bed +++ /dev/null @@ -1,9 +0,0 @@ -7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 -12 25378542 25378712 KRAS(NM_004985.3):c.450+6_c.291-5 -12 25380162 25380351 KRAS(NM_004985.3):c.290+6_c.112-5 -12 25398202 25398323 KRAS(NM_004985.3):c.111+6_c.-5 diff --git a/hotspot_variants/Melanoma.bed b/hotspot_variants/Melanoma.bed deleted file mode 100644 index cae1b59..0000000 --- a/hotspot_variants/Melanoma.bed +++ /dev/null @@ -1,10 +0,0 @@ -1 115252184 115252354 NRAS(NM_002524.3):c.450+6_c.291-5 -1 115256415 115256604 NRAS(NM_002524.3):c.290+6_c.112-5 -1 115258665 115258786 NRAS(NM_002524.3):c.111+6_c.-5 -4 55592017 55592221 KIT(NM_000222.2):c.1347-5_1540+5 -4 55593576 55593713 KIT(NM_000222.2):c.1648-5_1774+5 -4 55594171 55594292 KIT(NM_000222.2):c.1880-5_1990+5 -4 55595495 55595656 KIT(NM_000222.2):c.1991-5_2141+5 -4 55599230 55599363 KIT(NM_000222.2):c.2362-5_2484+5 -7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 diff --git a/hotspot_variants/Thyroid.bed b/hotspot_variants/Thyroid.bed deleted file mode 100644 index 4cc2834..0000000 --- a/hotspot_variants/Thyroid.bed +++ /dev/null @@ -1,40 +0,0 @@ -1 115252184 115252354 NRAS(NM_002524.3):c.450+6_c.291-5(exon4) -1 115256415 115256604 NRAS(NM_002524.3):c.290+6_c.112-5(exon3) -1 115258665 115258786 NRAS(NM_002524.3):c.111+6_c.-5(exon2) -7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5(exon15) -10 43572701 43572784 RET(NM_020975.4):c.-5_73+5(exon1) -10 43595901 43596175 RET(NM_020975.4):c.74-5_337+5(exon2) -10 43597784 43598082 RET(NM_020975.4):c.338-5_625+5(exon3) -10 43600394 43600646 RET(NM_020975.4):c.626-5_867+5(exon4) -10 43601818 43602024 RET(NM_020975.4):c.868-5_1063+5(exon5) -10 43604473 43604683 RET(NM_020975.4):c.1064-5_1263+5(exon6) -10 43606649 43606918 RET(NM_020975.4):c.1264-5_1522+5(exon7) -10 43607541 43607677 RET(NM_020975.4):c.1523-5_1648+5(exon8) -10 43608295 43608416 RET(NM_020975.4):c.1649-5_1759+5(exon9) -10 43608998 43609128 RET(NM_020975.4):c.1760-5_1879+5(exon10) -10 43609922 43610189 RET(NM_020975.4):c.1880-5_2136+5(exon11) -10 43612026 43612184 RET(NM_020975.4):c.2137-5_2284+5(exon12) -10 43613815 43613933 RET(NM_020975.4):c.2285-5_2392+5(exon13) -10 43614973 43615198 RET(NM_020975.4):c.2393-5_2607+5(exon14) -10 43615523 43615656 RET(NM_020975.4):c.2608-5_2730+5(exon15) -10 43617388 43617469 RET(NM_020975.4):c.2731-5_2801+5(exon16) -10 43619113 43619261 RET(NM_020975.4):c.2802-5_2939+5(exon17) -10 43620325 43620435 RET(NM_020975.4):c.2940-5_3039+5(exon18) -10 43622017 43622175 RET(NM_020975.4):c.3040-5_3187+5(exon19) -10 43623554 43623722 RET(NM_020975.4):c.3188-5_*5(exon20) -11 533760 533949 HRAS(NM_005343.2):c.290+6_c.112-5(exon3) -11 534206 534327 HRAS(NM_005343.2):c.111+6_c.-5(exon2) -12 25378542 25378712 KRAS(NM_004985.3):c.450+6_c.291-5(exon4) -12 25380162 25380351 KRAS(NM_004985.3):c.290+6_c.112-5(exon3) -12 25398202 25398323 KRAS(NM_004985.3):c.111+6_c.-5(exon2) -17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5(exon11) -17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5(exon10) -17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T(exon10alt) -17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5(exon9) -17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5(exon8) -17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5(exon7) -17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5(exon6) -17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5(exon5) -17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5(exon4) -17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5(exon3) -17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5(exon2) diff --git a/hotspot_variants/Tumour.bed b/hotspot_variants/Tumour.bed deleted file mode 100644 index aa0b80b..0000000 --- a/hotspot_variants/Tumour.bed +++ /dev/null @@ -1,194 +0,0 @@ -1 27022889 27024036 ARID1A(NM_006015.4):c.-6_1137+5 -1 27056136 27056359 ARID1A(NM_006015.4):c.1138-5_1350+5 -1 27057637 27058100 ARID1A(NM_006015.4):c.1351-5_1803+5 -1 27059161 27059288 ARID1A(NM_006015.4):c.1804-5_1920+5 -1 27087341 27087592 ARID1A(NM_006015.4):c.1921-5_2161+5 -1 27087869 27087969 ARID1A(NM_006015.4):c.2162-5_2251+5 -1 27088637 27088815 ARID1A(NM_006015.4):c.2252-5_2419+5 -1 27089458 27089781 ARID1A(NM_006015.4):c.2420-5_2732+5 -1 27092706 27092862 ARID1A(NM_006015.4):c.2733-5_2878+5 -1 27092942 27093062 ARID1A(NM_006015.4):c.2879-5_2988+5 -1 27094275 27094495 ARID1A(NM_006015.4):c.2989-5_3198+5 -1 27097604 27097822 ARID1A(NM_006015.4):c.3199-5_3406+5 -1 27098985 27099128 ARID1A(NM_006015.4):c.3407-5_3539+5 -1 27099297 27099483 ARID1A(NM_006015.4):c.3540-5_3715+5 -1 27099831 27099992 ARID1A(NM_006015.4):c.3716-5_3866+5 -1 27100065 27100213 ARID1A(NM_006015.4):c.3867-5_4004+5 -1 27100287 27100394 ARID1A(NM_006015.4):c.4005-5_4101+5 -1 27100814 27101716 ARID1A(NM_006015.4):c.4102-5_4993+5 -1 27102062 27102203 ARID1A(NM_006015.4):c.4994-5_5124+5 -1 27105508 27107252 ARID1A(NM_006015.4):c.5125-5_*5 -1 115252184 115252354 NRAS(NM_002524.3):c.450+6_c.291-5 -1 115256415 115256604 NRAS(NM_002524.3):c.290+6_c.112-5 -1 115258665 115258786 NRAS(NM_002524.3):c.111+6_c.-5 -1 226252024 226252185 H3F3A(NM_002107.4):c.-23-6_128+5 -2 209113087 209113389 IDH2(NM_005896.2):c.414+6_c.123-5 -3 178927968 178928131 PIK3CA(NM_006218.4):c.1252-5_1404+5(exon8) -3 178935992 178936127 PIK3CA(NM_006218.2):c.1540-5_1664+5 -3 178951876 178952157 PIK3CA(NM_006218.2):c.2937-5_*5 -4 55141002 55141145 PDGFRA(NM_006206.4):c.1654-5_1786+5 -4 55144057 55144178 PDGFRA(NM_006206.4):c.1892-5_2002+5 -4 55152002 55152135 PDGFRA(NM_006206.4):c.2440-5_2562+5 -4 55592017 55592221 KIT(NM_000222.2):c.1347-5_1540+5 -4 55593576 55593713 KIT(NM_000222.2):c.1648-5_1774+5 -4 55594171 55594292 KIT(NM_000222.2):c.1880-5_1990+5 -4 55595495 55595656 KIT(NM_000222.2):c.1991-5_2141+5 -4 55599230 55599363 KIT(NM_000222.2):c.2362-5_2484+5 -5 1295227 1295228 TERT(NM_198253.2):c.-124_-124 -5 1295249 1295250 TERT(NM_198253.2):c.-146_-146 -6 152265302 152265648 ESR1(NM_000125.3):c.761-6_c.1096+5 -6 152332785 152332934 ESR1(NM_000125.3):c.1097-6_c.1235+5 -6 152415514 152415638 ESR1(NM_000125.3):c.1370-6_c.1488 -6 152419861 152420106 ESR1(NM_000125.3):c.1554-6_c.*5 -7 55241608 55241741 EGFR(NM_005228.3):c.2062-5_2184+5 -7 55242409 55242518 EGFR(NM_005228.3):c.2185-5_2283+5 -7 55248980 55249176 EGFR(NM_005228.3):c.2284-5_2469+5 -7 55259406 55259572 EGFR(NM_005228.3):c.2470-5_2625+5 -7 140453069 140453198 BRAF(NM_004333.4):c.1742-5_1860+5 -7 140481370 140481498 BRAF(NM_004333.4):c.1315-5_1432+5 -9 21968222 21968246 CDKN2A(NM_000077.3):c.*6_458-5 -9 21970895 21971212 CDKN2A(NM_000077.3):c.151-5_457+5 -9 21974671 21974831 CDKN2A(NM_000077.3):c.150+5_-5 -10 43572701 43572784 RET(NM_020975.4):c.-5_73+5 -10 43595901 43596175 RET(NM_020975.4):c.74-5_337+5 -10 43597784 43598082 RET(NM_020975.4):c.338-5_625+5 -10 43600394 43600646 RET(NM_020975.4):c.626-5_867+5 -10 43601818 43602024 RET(NM_020975.4):c.868-5_1063+5 -10 43604473 43604683 RET(NM_020975.4):c.1064-5_1263+5 -10 43606649 43606918 RET(NM_020975.4):c.1264-5_1522+5 -10 43607541 43607677 RET(NM_020975.4):c.1523-5_1648+5 -10 43608295 43608416 RET(NM_020975.4):c.1649-5_1759+5 -10 43608998 43609128 RET(NM_020975.4):c.1760-5_1879+5 -10 43609922 43610189 RET(NM_020975.4):c.1880-5_2136+5 -10 43612026 43612184 RET(NM_020975.4):c.2137-5_2284+5 -10 43613815 43613933 RET(NM_020975.4):c.2285-5_2392+5 -10 43614973 43615198 RET(NM_020975.4):c.2393-5_2607+5 -10 43615523 43615656 RET(NM_020975.4):c.2608-5_2730+5 -10 43617388 43617469 RET(NM_020975.4):c.2731-5_2801+5 -10 43619113 43619261 RET(NM_020975.4):c.2802-5_2939+5 -10 43620325 43620435 RET(NM_020975.4):c.2940-5_3039+5 -10 43622017 43622175 RET(NM_020975.4):c.3040-5_3187+5 -10 43623554 43623722 RET(NM_020975.4):c.3188-5_*5 -10 89624221 89624310 PTEN(NM_000314.4):c.-6_79+5 -10 89653776 89653871 PTEN(NM_000314.4):c.80-5_164+5 -10 89685264 89685319 PTEN(NM_000314.4):c.165-5_209+5 -10 89690797 89690851 PTEN(NM_000314.4):c.210-5_253+5 -10 89692764 89693013 PTEN(NM_000314.4):c.254-5_492+5 -10 89711869 89712021 PTEN(NM_000314.4):c.493-5_634+5 -10 89717604 89717781 PTEN(NM_000314.4):c.635-5_801+5 -10 89720645 89720880 PTEN(NM_000314.4):c.802-5_1026+5 -10 89725038 89725234 PTEN(NM_000314.4):c.1027-5_*5 -11 533760 533949 NM_005343.2(HRAS):c.290+6_c.112-5 -11 534206 534327 NM_005343.2(HRAS):c.111+6_c.-5 -12 25378542 25378712 KRAS(NM_004985.3):c.450+6_c.291-5 -12 25380162 25380351 KRAS(NM_004985.3):c.290+6_c.112-5 -12 25398202 25398323 KRAS(NM_004985.3):c.111+6_c.-5 -13 32890577 32890684 BRCA2(NM_000059.3):c.1-21_67+20 -13 32893193 32893482 BRCA2(NM_000059.3):c.68-20_316+20 -13 32899192 32899341 BRCA2(NM_000059.3):c.317-20_425+20 -13 32900217 32900307 BRCA2(NM_000059.3):c.426-20_475+20 -13 32900358 32900439 BRCA2(NM_000059.3):c.476-20_516+20 -13 32900615 32900770 BRCA2(NM_000059.3):c.517-20_631+20 -13 32903559 32903649 BRCA2(NM_000059.3):c.632-20_681+20 -13 32905035 32905187 BRCA2(NM_000059.3):c.682-20_793+20 -13 32906388 32907534 BRCA2(NM_000059.3):c.794-20_1909+20 -13 32910381 32915353 BRCA2(NM_000059.3):c.1910-20_6841+20 -13 32918674 32918810 BRCA2(NM_000059.3):c.6842-20_6937+20 -13 32920943 32921053 BRCA2(NM_000059.3):c.6938-20_7007+20 -13 32928977 32929445 BRCA2(NM_000059.3):c.7008-20_7435+20 -13 32930544 32930766 BRCA2(NM_000059.3):c.7436-20_7617+20 -13 32931858 32932086 BRCA2(NM_000059.3):c.7618-20_7805+20 -13 32936639 32936850 BRCA2(NM_000059.3):c.7806-20_7976+20 -13 32937295 32937690 BRCA2(NM_000059.3):c.7977-20_8331+20 -13 32944518 32944714 BRCA2(NM_000059.3):c.8332-20_8487+20 -13 32945072 32945257 BRCA2(NM_000059.3):c.8488-20_8632+20 -13 32950786 32950948 BRCA2(NM_000059.3):c.8633-20_8754+20 -13 32953433 32953672 BRCA2(NM_000059.3):c.8755-20_8953+20 -13 32953866 32954070 BRCA2(NM_000059.3):c.8954-20_9117+20 -13 32954123 32954302 BRCA2(NM_000059.3):c.9118-20_9256+20 -13 32968805 32969090 BRCA2(NM_000059.3):c.9257-20_9501+20 -13 32971014 32971201 BRCA2(NM_000059.3):c.9502-20_9648+20 -13 32972278 32972927 BRCA2(NM_000059.3):c.9649-20_*20 -15 90631813 90631984 IDH2(NM_002168.2):c.534+6_c.374-5 -17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5 -17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5 -17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T -17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5 -17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5 -17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5 -17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5 -17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5 -17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5 -17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5 -17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5 -17 37868175 37868305 ERBB2(NM_004448.2):c.902-6_c.1021+5 -17 37879566 37879715 ERBB2(NM_004448.2):c.1947-6_c.2085+5 -17 37880159 37880268 ERBB2(NM_004448.2):c.2209-6_c.2307+5 -17 37880973 37881169 ERBB2(NM_004448.2):c.2308-6_c.2493+5 -17 37881296 37881462 ERBB2(NM_004448.2):c.2494-6_c.2649+5 -17 37881574 37881660 ERBB2(NM_004448.2):c.2650-6_2725+5 -17 41197674 41197839 BRCA1(NM_007294.3):c.5468-20_*20 -17 41199639 41199740 BRCA1(NM_007294.3):c.5407-20_5467+20 -17 41201117 41201231 BRCA1(NM_007294.3):c.5333-20_5406+20 -17 41203059 41203154 BRCA1(NM_007294.3):c.5278-20_5332+20 -17 41209048 41209172 BRCA1(NM_007294.3):c.5194-20_5277+20 -17 41215329 41215410 BRCA1(NM_007294.3):c.5153-20_5193+20 -17 41215870 41215988 BRCA1(NM_007294.3):c.5075-20_5152+20 -17 41219604 41219732 BRCA1(NM_007294.3):c.4987-20_5074+20 -17 41222924 41223275 BRCA1(NM_007294.3):c.4676-20_4986+20 -17 41226327 41226558 BRCA1(NM_007294.3):c.4485-20_4675+20 -17 41228484 41228651 BRCA1(NM_007294.3):c.4358-20_4484+20 -17 41234400 41234612 BRCA1(NM_007294.3):c.4186-20_4357+20 -17 41242940 41243069 BRCA1(NM_007294.3):c.4097-20_4185+20 -17 41243431 41246897 BRCA1(NM_007294.3):c.671-20_4096+20 -17 41247842 41247959 BRCA1(NM_007294.3):c.594-20_670+20 -17 41249240 41249326 BRCA1(NM_007294.3):c.548-20_593+20 -17 41251771 41251917 BRCA1(NM_007294.3):c.442-20_547+20 -17 41256118 41256298 BRCA1(NM_007294.3):c.302-20_441+20 -17 41256864 41256993 BRCA1(NM_007294.3):c.213-20_301+20 -17 41258452 41258570 BRCA1(NM_007294.3):c.135-20_212+20 -17 41267722 41267816 BRCA1(NM_007294.3):c.81-20_134+20 -17 41276013 41276133 BRCA1(NM_007294.3):c.1-20_80+20 -X 66764983 66766609 AR(NM_000044.2):c.-6_1616+5 -X 66863092 66863254 AR(NM_000044.2):c.1617-5_1768+5 -X 66905846 66905973 AR(NM_000044.2):c.1769-5_1885+5 -X 66931238 66931536 AR(NM_000044.2):c.1886-5_2173+5 -X 66937314 66937469 AR(NM_000044.2):c.2174-5_2318+5 -X 66941669 66941810 AR(NM_000044.2):c.2319-5_2449+5 -X 66942663 66942831 AR(NM_000044.2):c.2450-5_2607+5 -X 66943522 66943688 AR(NM_000044.2):c.2608-5_*5 -X 76763824 76764113 ATRX(NM_000489.3):c.7201-6_c*5 -X 76776260 76776399 ATRX(NM_000489.3):c.7072-5_7200+5 -X 76776875 76776981 ATRX(NM_000489.3):c.6976-5_7071+5 -X 76777735 76777871 ATRX(NM_000489.3):c.6850-5_6975+5 -X 76778724 76778884 ATRX(NM_000489.3):c.6700-5_6849+5 -X 76812916 76813121 ATRX(NM_000489.3):c.6505-5_6699+5 -X 76814134 76814322 ATRX(NM_000489.3):c.6327-5_6504+5 -X 76829709 76829828 ATRX(NM_000489.3):c.6218-5_6326+5 -X 76845298 76845415 ATRX(NM_000489.3):c.6111-5_6217+5 -X 76849160 76849324 ATRX(NM_000489.3):c.5957-5_6110+5 -X 76854874 76855054 ATRX(NM_000489.3):c.5787-5_5956+5 -X 76855195 76855294 ATRX(NM_000489.3):c.5698-5_5786+5 -X 76855897 76856038 ATRX(NM_000489.3):c.5567-5_5697+5 -X 76872075 76872203 ATRX(NM_000489.3):c.5449-5_5566+5 -X 76874268 76874454 ATRX(NM_000489.3):c.5273-5_5448+5 -X 76875857 76876005 ATRX(NM_000489.3):c.5135-5_5272+5 -X 76888689 76888877 ATRX(NM_000489.3):c.4957-5_5134+5 -X 76889048 76889205 ATRX(NM_000489.3):c.4810-5_4956+5 -X 76890079 76890199 ATRX(NM_000489.3):c.4700-5_4809+5 -X 76891400 76891552 ATRX(NM_000489.3):c.4558-5_4699+5 -X 76907598 76907848 ATRX(NM_000489.3):c.4318-5_4557+5 -X 76909582 76909695 ATRX(NM_000489.3):c.4215-5_4317+5 -X 76912044 76912148 ATRX(NM_000489.3):c.4121-5_4214+5 -X 76918865 76919052 ATRX(NM_000489.3):c.3944-5_4120+5 -X 76920128 76920272 ATRX(NM_000489.3):c.3810-5_3943+5 -X 76931715 76931798 ATRX(NM_000489.3):c.3737-5_3809+5 -X 76937006 76940090 ATRX(NM_000489.3):c.663-5_3736+5 -X 76940425 76940503 ATRX(NM_000489.3):c.595-5_662+5 -X 76944305 76944425 ATRX(NM_000489.3):c.485-5_594+5 -X 76949307 76949431 ATRX(NM_000489.3):c.371-5_484+5 -X 76952059 76952197 ATRX(NM_000489.3):c.243-5_370+5 -X 76953065 76953128 ATRX(NM_000489.3):c.190-5_242+5 -X 76954056 76954122 ATRX(NM_000489.3):c.134-5_189+5 -X 76972602 76972725 ATRX(NM_000489.3):c.21-5_133+5 -X 77041462 77041492 ATRX(NM_000489.3):c.-5_20+5 diff --git a/hotspot_variants/aitcl.bed b/hotspot_variants/aitcl.bed deleted file mode 100644 index ad38434..0000000 --- a/hotspot_variants/aitcl.bed +++ /dev/null @@ -1,35 +0,0 @@ -2 25457142 25457294 DNMT3A(NM_175629.2):exon_23 -2 25458570 25458699 DNMT3A(NM_175629.2):exon_22 -2 25459799 25459879 DNMT3A(NM_175629.2):exon_21 -2 25461993 25462089 DNMT3A(NM_175629.2):exon_20 -2 25463165 25463324 DNMT3A(NM_175629.2):exon_19 -2 25463503 25463604 DNMT3A(NM_175629.2):exon_18 -2 25464425 25464581 DNMT3A(NM_175629.2):exon_17 -2 25466761 25466856 DNMT3A(NM_175629.2):exon_16 -2 25467018 25467212 DNMT3A(NM_175629.2):exon_15 -2 25467403 25467526 DNMT3A(NM_175629.2):exon_14 -2 25468116 25468206 DNMT3A(NM_175629.2):exon_13 -2 25468883 25468938 DNMT3A(NM_175629.2):exon_12 -2 25469023 25469183 DNMT3A(NM_175629.2):exon_11 -2 25469483 25469650 DNMT3A(NM_175629.2):exon_10 -2 25469914 25470032 DNMT3A(NM_175629.2):exon_9 -2 25470454 25470623 DNMT3A(NM_175629.2):exon_8 -2 25470900 25471126 DNMT3A(NM_175629.2):exon_7 -2 25472520 25472598 DNMT3A(NM_153759.3):exon_2 -2 25475057 25475071 DNMT3A(NM_153759.3):exon_1 -2 25497804 25497961 DNMT3A(NM_175629.2):exon_6 -2 25498363 25498417 DNMT3A(NM_175629.2):exon_5 -2 25505304 25505585 DNMT3A(NM_175629.2):exon_4 -2 25523002 25523117 DNMT3A(NM_175629.2):exon_3 -2 25536776 25536858 DNMT3A(NM_175629.2):exon_2 -3 49412861 49413027 RHOA(NM_001664.3):exon_2 -4 106155094 106158602 TET2(NM_001127208.2):exon_3 -4 106162490 106162591 TET2(NM_001127208.2):exon_4 -4 106163985 106164089 TET2(NM_001127208.2):exon_5 -4 106164721 106164940 TET2(NM_001127208.2):exon_6 -4 106180770 106180931 TET2(NM_001127208.2):exon_7 -4 106182910 106183010 TET2(NM_001127208.2):exon_8 -4 106190761 106190909 TET2(NM_001127208.2):exon_9 -4 106193715 106194080 TET2(NM_001127208.2):exon_10 -4 106196199 106197681 TET2(NM_001127208.2):exon_11 -15 90631813 90631984 IDH2(NM_002168.3):exon_4 diff --git a/hotspot_variants/aml.bed b/hotspot_variants/aml.bed deleted file mode 100644 index 1cbd5dd..0000000 --- a/hotspot_variants/aml.bed +++ /dev/null @@ -1,17 +0,0 @@ -2 209113104 209113119 IDH1(NM_005896.3):codon_R132 -5 170837525 170837574 NPM1(NM_002520.6):exon_11 -13 28592598 28592731 FLT3(NM_004119.2):exon_20 -13 28608018 28608133 FLT3(NM_004119.2):exon_15 -13 28608213 28608356 FLT3(NM_004119.2):exon_14 -13 28608432 28608549 FLT3(NM_004119.2):exon_13 -15 90631813 90631984 IDH2(NM_002168.3):exon_4 -17 7572921 7573013 TP53(NM_000546.5):exon_11 -17 7573921 7574038 TP53(NM_000546.5):exon_10 -17 7576847 7576931 TP53(NM_000546.5):exon_9 -17 7577013 7577160 TP53(NM_000546.5):exon_8 -17 7577493 7577613 TP53(NM_000546.5):exon_7 -17 7578171 7578294 TP53(NM_000546.5):exon_6 -17 7578365 7578559 TP53(NM_000546.5):exon_5 -17 7579306 7579595 TP53(NM_000546.5):exon_4 -17 7579694 7579726 TP53(NM_000546.5):exon_3 -17 7579833 7579917 TP53(NM_000546.5):exon_2 diff --git a/hotspot_variants/breast.bed b/hotspot_variants/breast.bed deleted file mode 100755 index af599e9..0000000 --- a/hotspot_variants/breast.bed +++ /dev/null @@ -1,3 +0,0 @@ -3 178927968 178928131 PIK3CA(NM_006218.4):c.1252-5_1404+5(exon8) -3 178935992 178936127 PIK3CA(NM_006218.4):c.1540-5_1664+5(exon10) -3 178951876 178952157 PIK3CA(NM_006218.4):c.2937-5_3207+5(exon21) diff --git a/hotspot_variants/cll.bed b/hotspot_variants/cll.bed deleted file mode 100644 index 18b4a1a..0000000 --- a/hotspot_variants/cll.bed +++ /dev/null @@ -1,10 +0,0 @@ -17 7572921 7573013 TP53(NM_000546.5):exon_11 -17 7573921 7574038 TP53(NM_000546.5):exon_10 -17 7576847 7576931 TP53(NM_000546.5):exon_9 -17 7577013 7577160 TP53(NM_000546.5):exon_8 -17 7577493 7577613 TP53(NM_000546.5):exon_7 -17 7578171 7578294 TP53(NM_000546.5):exon_6 -17 7578365 7578559 TP53(NM_000546.5):exon_5 -17 7579306 7579595 TP53(NM_000546.5):exon_4 -17 7579694 7579726 TP53(NM_000546.5):exon_3 -17 7579833 7579917 TP53(NM_000546.5):exon_2 diff --git a/hotspot_variants/endometrial-pole-tp53.bed b/hotspot_variants/endometrial-pole-tp53.bed deleted file mode 100644 index b09d621..0000000 --- a/hotspot_variants/endometrial-pole-tp53.bed +++ /dev/null @@ -1,17 +0,0 @@ -12 133249744 133249868 POLE(NM006231.3):c.1473+5_c.1360-5(exon14) -12 133250155 133250298 POLE(NM006231.3):c.1359+5_c.1227-5(exon13) -12 133251978 133252108 POLE(NM006231.3):c.1226+5_c.1107-5(exon12) -12 133252315 133252411 POLE(NM006231.3):c.1106+5_c.1021-5(exon11) -12 133252674 133252795 POLE(NM006231.3):c.1020+5_c.910-5(exon10) -12 133253126 133253244 POLE(NM006231.3):c.909+5_c.802-5(exon9) -17 7572921 7573013 TP53(NM_000546.4):c.1101-5_*5(exon11) -17 7573921 7574038 TP53(NM_000546.4):c.994-5_1100+5(exon10) -17 7576524 7576671 TP53(NM_001276695.1):c.*12+1C>T_(NM_001276696.1):c.877-14C>T(exon10alt) -17 7576847 7576931 TP53(NM_000546.4):c.920-5_993+5(exon9) -17 7577013 7577160 TP53(NM_000546.4):c.783-5_919+5(exon8) -17 7577493 7577613 TP53(NM_000546.4):c.673-5_782+5(exon7) -17 7578171 7578294 TP53(NM_000546.4):c.560-5_672+5(exon6) -17 7578365 7578559 TP53(NM_000546.4):c.376-5_559+5(exon5) -17 7579306 7579595 TP53(NM_000546.4):c.97-5_375+5(exon4) -17 7579694 7579726 TP53(NM_000546.4):c.75-5_96+5(exon3) -17 7579833 7579945 TP53(NM_000546.4):c.-28-5_74+5(exon2) diff --git a/hotspot_variants/endometrial-pole.bed b/hotspot_variants/endometrial-pole.bed deleted file mode 100644 index 8bb40fa..0000000 --- a/hotspot_variants/endometrial-pole.bed +++ /dev/null @@ -1,6 +0,0 @@ -12 133249744 133249868 POLE(NM006231.3):c.1473+5_c.1360-5(exon14) -12 133250155 133250298 POLE(NM006231.3):c.1359+5_c.1227-5(exon13) -12 133251978 133252108 POLE(NM006231.3):c.1226+5_c.1107-5(exon12) -12 133252315 133252411 POLE(NM006231.3):c.1106+5_c.1021-5(exon11) -12 133252674 133252795 POLE(NM006231.3):c.1020+5_c.910-5(exon10) -12 133253126 133253244 POLE(NM006231.3):c.909+5_c.802-5(exon9) diff --git a/hotspot_variants/fight-209.bed b/hotspot_variants/fight-209.bed deleted file mode 100644 index 10e3ec6..0000000 --- a/hotspot_variants/fight-209.bed +++ /dev/null @@ -1,57 +0,0 @@ -4 1803245 1803248 FGFR3(NM_000142.4):codon_R200 -4 1803563 1803566 FGFR3(NM_000142.4):codon_R248 -4 1803566 1803569 FGFR3(NM_000142.4):codon_S249 -4 1805511 1805514 FGFR3(NM_000142.4):codon_G342 -4 1806056 1806247 FGFR3(NM_000142.4):exon_9 -4 1806088 1806091 FGFR3(NM_000142.4):codon_G370 -4 1806091 1806094 FGFR3(NM_000142.4):codon_S371 -4 1806097 1806100 FGFR3(NM_000142.4):codon_Y373 -4 1806103 1806106 FGFR3(NM_000142.4):codon_G375 -4 1806118 1806121 FGFR3(NM_000142.4):codon_G380 -4 1806151 1806154 FGFR3(NM_000142.4):codon_A391 -4 1807332 1807335 FGFR3(NM_000142.4):codon_M528 -4 1807368 1807371 FGFR3(NM_000142.4):codon_N540 -4 1807493 1807496 FGFR3(NM_000142.4):codon_V555 -4 1807801 1807804 FGFR3(NM_000142.4):codon_R621 -4 1807861 1807864 FGFR3(NM_000142.4):codon_D641 -4 1807888 1807891 FGFR3(NM_000142.4):codon_K650 -8 38285492 38285495 FGFR1(NM_023110.2):codon_R189 -8 38282206 38282209 FGFR1(NM_023110.2):codon_P252 -8 38277212 38277215 FGFR1(NM_023110.2):codon_Y374 -8 38277191 38277194 FGFR1(NM_023110.2):codon_C381 -8 38275840 38275843 FGFR1(NM_023110.2):codon_R445 -8 38274848 38274851 FGFR1(NM_023110.2):codon_N546 -8 38273558 38273561 FGFR1(NM_023110.2):codon_V561 -8 38272305 38272308 FGFR1(NM_023110.2):codon_K656 -10 123310899 123310929 FGFR2(NM_000141.4):exon_5_partial_p167-176 -10 123310818 123310821 FGFR2(NM_000141.4):codon_R203 -10 123298223 123298226 FGFR2(NM_000141.4):codon_R210 -10 123279675 123279678 FGFR2(NM_000141.4):codon_S252 -10 123279672 123279675 FGFR2(NM_000141.4):codon_P253 -10 123279612 123279666 FGFR2(NM_000141.4):exon_7_partial_p256-273 -10 123279630 123279633 FGFR2(NM_000141.4):codon_S267 -10 123279561 123279564 FGFR2(NM_000141.4):codon_W290 -10 123279495 123279594 FGFR2(NM_000141.4):exon_7_partial_p280-312 -10 123276971 123276974 FGFR2(NM_000141.4):codon_A315 -10 123276908 123276911 FGFR2(NM_000141.4):codon_D336 -10 123276890 123276893 FGFR2(NM_000141.4):codon_C342 -10 123276875 123276878 FGFR2(NM_000141.4):codon_S347 -10 123276863 123276866 FGFR2(NM_000141.4):codon_S351 -10 123276854 123276857 FGFR2(NM_000141.4):codon_S354 -10 123274801 123274804 FGFR2(NM_000141.4):codon_S372 -10 123274792 123274795 FGFR2(NM_000141.4):codon_Y375 -10 123274771 123274774 FGFR2(NM_000141.4):codon_C382 -10 123274744 123274747 FGFR2(NM_000141.4):codon_M391 -10 123274732 123274735 FGFR2(NM_000141.4):codon_V395 -10 123258069 123258072 FGFR2(NM_000141.4):codon_M537 -10 123258039 123258042 FGFR2(NM_000141.4):codon_I547 -10 123258033 123258036 FGFR2(NM_000141.4):codon_N549 -10 123256216 123256219 FGFR2(NM_000141.4):codon_V564 -10 123256213 123256216 FGFR2(NM_000141.4):codon_E565 -10 123256201 123256204 FGFR2(NM_000141.4):codon_K569 -10 123256057 123256060 FGFR2(NM_000141.4):codon_L617 -10 123247582 123247585 FGFR2(NM_000141.4):codon_E636 -10 123247567 123247570 FGFR2(NM_000141.4):codon_K641 -10 123247513 123247516 FGFR2(NM_000141.4):codon_K659 -10 123246932 123246935 FGFR2(NM_000141.4):codon_R664 -10 123246890 123246893 FGFR2(NM_000141.4):codon_R678 diff --git a/hotspot_variants/mpn.bed b/hotspot_variants/mpn.bed deleted file mode 100644 index dd1c653..0000000 --- a/hotspot_variants/mpn.bed +++ /dev/null @@ -1,4 +0,0 @@ -1 43814928 43815035 MPL(NM_005373.2):exon_10 -9 5069919 5070057 JAK2(NM_004972.3):exon_12) -9 5073763 5073778 JAK2(NM_004972.3):codon_V617) -19 13054521 13054732 CALR(NM_004343.3):exon_9 diff --git a/hotspot_variants/myeloid.bed b/hotspot_variants/myeloid.bed deleted file mode 100644 index 0d3eeba..0000000 --- a/hotspot_variants/myeloid.bed +++ /dev/null @@ -1,130 +0,0 @@ -1 43814928 43815035 MPL(NM_005373.2):exon_10 -1 115256521 115256536 NRAS(NM_002524.4):codon_Q61 -1 115258736 115258754 NRAS(NM_002524.4):codons_G12-13 -2 25457142 25457294 DNMT3A(NM_175629.2):exon_23 -2 25458570 25458699 DNMT3A(NM_175629.2):exon_22 -2 25459799 25459879 DNMT3A(NM_175629.2):exon_21 -2 25461993 25462089 DNMT3A(NM_175629.2):exon_20 -2 25463165 25463324 DNMT3A(NM_175629.2):exon_19 -2 25463503 25463604 DNMT3A(NM_175629.2):exon_18 -2 25464425 25464581 DNMT3A(NM_175629.2):exon_17 -2 25466761 25466856 DNMT3A(NM_175629.2):exon_16 -2 25467018 25467212 DNMT3A(NM_175629.2):exon_15 -2 25467403 25467526 DNMT3A(NM_175629.2):exon_14 -2 25468116 25468206 DNMT3A(NM_175629.2):exon_13 -2 25468883 25468938 DNMT3A(NM_175629.2):exon_12 -2 25469023 25469183 DNMT3A(NM_175629.2):exon_11 -2 25469483 25469650 DNMT3A(NM_175629.2):exon_10 -2 25469914 25470032 DNMT3A(NM_175629.2):exon_9 -2 25470454 25470623 DNMT3A(NM_175629.2):exon_8 -2 25470900 25471126 DNMT3A(NM_175629.2):exon_7 -2 25472520 25472598 DNMT3A(NM_153759.3):exon_2 -2 25475057 25475071 DNMT3A(NM_153759.3):exon_1 -2 25497804 25497961 DNMT3A(NM_175629.2):exon_6 -2 25498363 25498417 DNMT3A(NM_175629.2):exon_5 -2 25505304 25505585 DNMT3A(NM_175629.2):exon_4 -2 25523002 25523117 DNMT3A(NM_175629.2):exon_3 -2 25536776 25536858 DNMT3A(NM_175629.2):exon_2 -2 198266460 198266617 SF3B1(NM_012433.3):exon_16 -2 198266703 198266859 SF3B1(NM_012433.3):exon_15 -2 198267274 198267555 SF3B1(NM_012433.3):exon_14 -2 198267667 198267764 SF3B1(NM_012433.3):exon_13 -2 209113104 209113119 IDH1(NM_005896.3):codon_R132 -3 128199856 128200166 GATA2(NM_032638.4):exon_6 -3 128200656 128200792 GATA2(NM_032638.4):exon_5 -3 128202697 128202853 GATA2(NM_032638.4):exon_4 -3 128204564 128205216 GATA2(NM_032638.4):exon_3 -3 128205640 128205879 GATA2(NM_032638.4):exon_2 -4 55141002 55141145 PDGFRA(NM_006206.5):exon_12 -4 55144057 55144178 PDGFRA(NM_006206.5):exon_14 -4 55152002 55152135 PDGFRA(NM_006206.5):exon_18 -4 55599230 55599363 KIT(NM_000222.2):exon_17 -4 106155094 106158602 TET2(NM_001127208.2):exon_3 -4 106162490 106162591 TET2(NM_001127208.2):exon_4 -4 106163985 106164089 TET2(NM_001127208.2):exon_5 -4 106164721 106164940 TET2(NM_001127208.2):exon_6 -4 106180770 106180931 TET2(NM_001127208.2):exon_7 -4 106182910 106183010 TET2(NM_001127208.2):exon_8 -4 106190761 106190909 TET2(NM_001127208.2):exon_9 -4 106193715 106194080 TET2(NM_001127208.2):exon_10 -4 106196199 106197681 TET2(NM_001127208.2):exon_11 -5 170837525 170837574 NPM1(NM_002520.6):exon_11 -7 148504732 148504803 EZH2(NM_004456.4):exon_20 -7 148506157 148506252 EZH2(NM_004456.4):exon_19 -7 148506396 148506487 EZH2(NM_004456.4):exon_18 -7 148507419 148507511 EZH2(NM_004456.4):exon_17 -7 148508711 148508817 EZH2(NM_004456.4):exon_16 -7 148511045 148511234 EZH2(NM_004456.4):exon_15 -7 148512000 148512136 EZH2(NM_004456.4):exon_14 -7 148512592 148512643 EZH2(NM_004456.4):exon_13 -7 148513770 148513875 EZH2(NM_004456.4):exon_12 -7 148514308 148514488 EZH2(NM_004456.4):exon_11 -7 148514963 148515214 EZH2(NM_004456.4):exon_10 -7 148516682 148516784 EZH2(NM_004456.4):exon_9 -7 148523540 148523729 EZH2(NM_004456.4):exon_8 -7 148524250 148524363 EZH2(NM_004456.4):exon_7 -7 148525826 148525977 EZH2(NM_004456.4):exon_6 -7 148526814 148526945 EZH2(NM_004456.4):exon_5 -7 148529720 148529847 EZH2(NM_004456.4):exon_4 -7 148543556 148543695 EZH2(NM_004456.4):exon_3 -7 148544268 148544395 EZH2(NM_004456.4):exon_2 -9 5069919 5070057 JAK2(NM_004972.3):exon_12 -9 5073763 5073778 JAK2(NM_004972.3):codon_V617 -9 139390517 139392015 NOTCH1(NM_017617.4):exon_34 -11 119148870 119149012 CBL(NM_005188.3):exon_8 -11 119149214 119149428 CBL(NM_005188.3):exon_9 -12 11803056 11803099 ETV6(NM_001987.4):exon_1 -12 11905378 11905518 ETV6(NM_001987.4):exon_2 -12 11992068 11992243 ETV6(NM_001987.4):exon_3 -12 12006355 12006500 ETV6(NM_001987.4):exon_4 -12 12022352 12022908 ETV6(NM_001987.4):exon_5 -12 12037373 12037526 ETV6(NM_001987.4):exon_6 -12 12038854 12038965 ETV6(NM_001987.4):exon_7 -12 12043869 12043985 ETV6(NM_001987.4):exon_8 -12 25380162 25380351 KRAS(NM_033360.3):exon_3 -12 25398202 25398323 KRAS(NM_033360.3):exon_2 -13 28592598 28592731 FLT3(NM_004119.2):exon_20 -13 28608018 28608133 FLT3(NM_004119.2):exon_15 -13 28608213 28608356 FLT3(NM_004119.2):exon_14 -13 28608432 28608549 FLT3(NM_004119.2):exon_13 -15 90631813 90631984 IDH2(NM_002168.3):exon_4 -17 7572921 7573013 TP53(NM_000546.5):exon_11 -17 7573921 7574038 TP53(NM_000546.5):exon_10 -17 7576847 7576931 TP53(NM_000546.5):exon_9 -17 7577013 7577160 TP53(NM_000546.5):exon_8 -17 7577493 7577613 TP53(NM_000546.5):exon_7 -17 7578171 7578294 TP53(NM_000546.5):exon_6 -17 7578365 7578559 TP53(NM_000546.5):exon_5 -17 7579306 7579595 TP53(NM_000546.5):exon_4 -17 7579694 7579726 TP53(NM_000546.5):exon_3 -17 7579833 7579917 TP53(NM_000546.5):exon_2 -17 74732875 74733247 SRSF2(NM_003016.4):exon_1 -18 42531876 42532065 SETBP1(NM_015559.2):exon_4_(partial) -19 13054521 13054732 CALR(NM_004343.3):exon_9 -19 33792238 33793325 CEBPA(NM_004364.4):exon_1 -20 31022229 31025146 ASXL1(NM_015338.5):exon_13 -21 36164426 36164912 RUNX1(NM_001754.4):exon_9 -21 36171592 36171764 RUNX1(NM_001754.4):exon_8 -21 36193959 36193998 RUNX1(NM_001122607.1):exon_5 -21 36206701 36206903 RUNX1(NM_001754.4):exon_7 -21 36231765 36231880 RUNX1(NM_001754.4):exon_6 -21 36252848 36253015 RUNX1(NM_001754.4):exon_5 -21 36259134 36259414 RUNX1(NM_001754.4):exon_4 -21 36265216 36265265 RUNX1(NM_001754.4):exon_3 -21 36421133 36421201 RUNX1(NM_001754.4):exon_2 -21 44514769 44514784 U2AF1(NM_006758.2):codon_Q157 -21 44524448 44524463 U2AF1(NM_006758.2):codon_S34 -X 39911356 39911658 BCOR(NM_001123385.1):exon_15 -X 39913133 39913300 BCOR(NM_001123385.1):exon_14 -X 39913503 39913591 BCOR(NM_001123385.1):exon_13 -X 39914615 39914771 BCOR(NM_001123385.1):exon_12 -X 39916402 39916579 BCOR(NM_001123385.1):exon_11 -X 39921386 39921651 BCOR(NM_001123385.1):exon_10 -X 39921993 39922329 BCOR(NM_001123385.1):exon_9 -X 39922855 39923210 BCOR(NM_001123385.1):exon_8 -X 39923583 39923857 BCOR(NM_001123385.1):exon_7 -X 39930220 39930417 BCOR(NM_001123385.1):exon_6 -X 39930884 39930948 BCOR(NM_001123385.1):exon_5 -X 39931596 39934438 BCOR(NM_001123385.1):exon_4 -X 39935701 39935790 BCOR(NM_001123385.1):exon_3 -X 39937091 39937187 BCOR(NM_001123385.1):exon_2 diff --git a/preferred_transcripts.txt b/preferred_transcripts.txt deleted file mode 100755 index 2285c7f..0000000 --- a/preferred_transcripts.txt +++ /dev/null @@ -1,38 +0,0 @@ -AR NM_000044.4 -ATRX NM_000489.4 -BRAF NM_004333.4 -BRCA1 NM_007294.3 -BRCA2 NM_000059.3 -CDKN2A NM_000077.4 -DPYD NM_000110.3 -EGFR NM_005228.3 -EML4 NM_019063.4 -ERBB2 NM_004448.3 -ESR1 NM_000125.3 -H3F3A NM_002107.4 -HRAS NM_005343.3 -IDH1 NM_005896.3 -IDH2 NM_002168.3 -KIT NM_000222.2 -KRAS NM_004985.4 -MET NM_001127500.1 -NRAS NM_002524.3 -NTRK1 NM_001007792.1 -PDGFRA NM_006206.4 -PIK3CA NM_006218.2 -PTEN NM_000314.4 -RET NM_020975.4 -ROS1 NM_002944.2 -TERT NM_198253.2 -TP53 NM_000546.5 -ARID1A NM_006015.5 -ALK NM_004304.3 -NTRK2 NM_006180.4 -NTRK3 NM_001012338.2 -KIF5B NM_004521.2 -CD74 NM_001025159.2 -SLC34A2 NM_006424.2 -EZR NM_001111077.1 -SDC4 NM_002999.3 -TPM3 NM_152263.2 -CCDC6 NM_005436.4 diff --git a/rerun_coverage.sh b/rerun_coverage.sh deleted file mode 100644 index 7440abc..0000000 --- a/rerun_coverage.sh +++ /dev/null @@ -1,267 +0,0 @@ -#!/bin/bash - -#SBATCH --time=24:00:00 -#SBATCH --output=%j-%N-rerun_coverage.out -#SBATCH --error=%j-%N-rerun_coverage.err -#SBATCH --partition=high - -#Description: Script to re-run coverage calculations for TSO500 App based pipeline when a sample has a new referral. # Can be just cov2json or from coverage calculator if the analysis folder is deleted. -# -#Usage: rerun_coverage.sh - -############################################################## -# Setup -############################################################## - -#Get variables from command line -run_id=$1 -sample=$2 -worksheet_id=$3 -referral=$4 - -output_path=/data/output/results/${run_id} - -# define filepaths for app -app_version=2.2.0 -app_dir=/data/diagnostics/pipelines/TSO500/illumina_app/TSO500_RUO_LocalApp-"$app_version" - -# define filepaths for post processing -pipeline_version=main -pipeline_dir=/data/diagnostics/pipelines/TSO500/TSO500_post_processing-"$pipeline_version" -pipeline_scripts="$pipeline_dir"/scripts - -# define pipeline variables -minimum_coverage="270 135" -coverage_bed_files_path="$pipeline_dir"/hotspot_coverage -vendor_capture_bed="$pipeline_dir"/vendorCaptureBed_100pad_updated.bed -preferred_transcripts="$pipeline_dir"/preferred_transcripts.txt - -#Load anaconda and environment -. ~/.bashrc -module load anaconda - -set +u -conda activate TSO500_post_processing -set -u - -#Check if analysis folder exists. -#If it does, check if referral was present at time of run. -#If not referral at time, or no analysis, start from DOC, otherwise run cov2json.py - -analysis_path=${output_path}/analysis - -if [ -d "$analysis_path" ]; -then - if [ -f "${analysis_path}/NTC-${worksheet_id}/depth_of_coverage/hotspot_coverage_135x/NTC-${worksheet_id}_${referral}_combined.coverage" ]; - then - analysis="True" - else - analysis="False" - fi -else - analysis="False" -fi - -#Run cov2json if analysis present, otherwise run from DOC -if [ $analysis = "True" ]; -then - - python "$pipeline_scripts"/coverage2json.py \ - --referral "$referral" \ - --groups_folder "$pipeline_dir"/hotspot_coverage/ \ - --sample_coverage "$analysis_path"/"$sample"/depth_of_coverage/ \ - --ntc_coverage "$analysis_path"/NTC-"$worksheet_id"/depth_of_coverage/ \ - --outfile "$output_path"/Gathered_Results/Database/"$sample"_"$referral"_coverage.json - - #Make new samplelist for upload - echo "${sample},${worksheet_id},DNA,$referral" > ${output_path}/Gathered_Results/Database/samples_database_${worksheet_id}_DNA_rereferral.csv - - -else - - bam_path="${output_path}/BAMs/" - - #Do everything for sample and NTC - for s_id in $sample NTC-${worksheet_id} - do - - depth_path="${output_path}/reanalysis/${s_id}/depth_of_coverage/" - mkdir ${output_path}/reanalysis - mkdir ${output_path}/reanalysis/${s_id} - mkdir ${output_path}/reanalysis/${s_id}/depth_of_coverage/ - - # reheader the bams to local area - java -jar /Apps/wren/picard/2.21.6/bin/picard.jar AddOrReplaceReadGroups \ - I="$bam_path"/"$s_id".bam \ - O="$bam_path"/"$s_id"_add_rg.bam \ - RGID=4 \ - RGLB=lib1 \ - RGPL=ILLUMINA \ - RGPU=unit1 \ - RGSM=20 - - # index new bam - samtools index "$bam_path"/"$s_id"_add_rg.bam "$bam_path"/"$s_id"_add_rg.bam.bai - - # run depth of coverage - gatk DepthOfCoverage \ - -I "$bam_path"/"$s_id"_add_rg.bam \ - -L "$vendor_capture_bed" \ - -R "$app_dir"/resources/genomes/hg19_hardPAR/genome.fa \ - -O "$depth_path"/"$s_id"_depth_of_coverage - - # change to tab delimited and remove colon from column 1 - sed 's/:/\t/g' "$depth_path"/"$s_id"_depth_of_coverage \ - | sed 's/,/\t/g' | grep -v 'Locus' \ - | sort -k1,1 -k2,2n | bgzip \ - > "$depth_path"/"$s_id"_depth_of_coverage.gz - - # tabix index depth of coverage file - tabix \ - -b 2 \ - -e 2 \ - -s 1 \ - "$depth_path"/"$s_id"_depth_of_coverage.gz - - # deactivate env - set +u - conda deactivate - set -u - - # Run coverage calculator for each coverage value - for min_coverage in $minimum_coverage; do - - # activate coverage calculator conda env - set +u - conda activate CoverageCalculatorPy - set -u - - # set output directory for coverage files - hscov_outdir=hotspot_coverage_"$min_coverage"x - - # run coverage calculator on each bed file - for bed_file in "$coverage_bed_files_path"/*.bed; do - - name=$(echo $(basename $bed_file) | cut -d"." -f1) - - python /data/diagnostics/apps/CoverageCalculatorPy/CoverageCalculatorPy-v1.1.0/CoverageCalculatorPy.py \ - -B "$coverage_bed_files_path"/"$name".bed \ - -D "$depth_path"/"$s_id"_depth_of_coverage.gz \ - --depth "$min_coverage" \ - --padding 0 \ - --groupfile "$coverage_bed_files_path"/"$name".groups \ - --outname "$s_id"_"$name" \ - --outdir "$depth_path"/"$hscov_outdir"/ - - # remove header from gaps file - if [[ $(wc -l < "$depth_path"/"$hscov_outdir"/"$s_id"_"$name".gaps) -eq 1 ]]; then - # no gaps - touch "$depth_path"/"$hscov_outdir"/"$s_id"_"$name".nohead.gaps - - else - # gaps - grep -v '^#' "$depth_path"/"$hscov_outdir"/"$s_id"_"$name".gaps > "$depth_path"/"$hscov_outdir"/"$s_id"_"$name".nohead.gaps - - fi - - # remove chr from bed file so bed2hgvs works - cat "$depth_path"/"$hscov_outdir"/"$s_id"_"$name".nohead.gaps | sed 's/^chr//' > "$depth_path"/"$hscov_outdir"/"$s_id"_"$name".nohead_nochr.gaps - - # remove intermediate files - rm "$depth_path"/"$hscov_outdir"/"$s_id"_"$name".gaps - rm "$depth_path"/"$hscov_outdir"/"$s_id"_"$name".nohead.gaps - - done - - - # activate bed2hgvs conda env - set +u - conda deactivate - conda activate bed2hgvs - set -u - - # run on each bed file - for gaps_file in "$depth_path"/"$hscov_outdir"/*.nohead_nochr.gaps; do - - name=$(echo $(basename $gaps_file) | cut -d"." -f1) - echo $name - - Rscript /data/diagnostics/apps/bed2hgvs/bed2hgvs-v0.3.0/bed2hgvs.R \ - --bedfile $gaps_file \ - --outname "$name".gaps \ - --outdir "$depth_path"/"$hscov_outdir" \ - --preferred_tx $preferred_transcripts - - # remove intermediate file - rm "$depth_path"/"$hscov_outdir"/"$name".nohead_nochr.gaps - done - - # combine all total coverage files - if [ -f "$depth_path"/"$hscov_outdir"/"$s_id"_coverage.txt ]; then rm "$depth_path"/"$hscov_outdir"/"$s_id"_coverage.txt; fi - cat "$depth_path"/"$hscov_outdir"/*.totalCoverage | grep "FEATURE" | head -n 1 >> "$depth_path"/"$hscov_outdir"/"$s_id"_coverage.txt - cat "$depth_path"/"$hscov_outdir"/*.totalCoverage | grep -v "FEATURE" | grep -vP "combined_\\S+_GENE" >> "$depth_path"/"$hscov_outdir"/"$s_id"_coverage.txt - - # deactivate env - set +u - conda deactivate - set -u - - - # activate conda env - set +u - conda activate TSO500_post_processing - set -u - - cosmic_tool_path=/data/diagnostics/apps/cosmic_gaps/cosmic_gaps-master - - gaps_file="$depth_path"/"$hscov_outdir"/"$s_id"_"$referral"_hotspots.gaps - - # hotspot gaps file may be missing for some referrals - if [[ -f $gaps_file ]] - then - - # only run bedtools intersect for certain referral types - if [ $referral = "Melanoma" ] || [ $referral = "Lung" ] || [ $referral = "Colorectal" ] || [ $referral = "GIST" ] || [ $referral = "breast" ] - then - dos2unix $gaps_file - - # find the overlap between the hotspots file and the referral file from cosmic - bedtools intersect \ - -loj \ - -F 1 \ - -a $gaps_file \ - -b "$cosmic_tool_path"/cosmic_bedfiles/"$referral".bed \ - -wao \ - > "$depth_path"/"$hscov_outdir"/"$s_id"_"$referral"_intersect.txt - - fi - - # filter the output - python "$cosmic_tool_path"/filter_table.py \ - --sampleId $s_id \ - --referral $referral \ - --gaps_path "$depth_path"/"$hscov_outdir"/ \ - --bedfile_path "$cosmic_tool_path"/cosmic_bedfiles/ - - fi - - #Remove copy of bam with read groups and index - rm "$bam_path"/"$s_id"_add_rg.bam* - done - done - - python "$pipeline_scripts"/coverage2json.py \ - --referral "$referral" \ - --groups_folder "$pipeline_dir"/hotspot_coverage/ \ - --sample_coverage "$output_path"/reanalysis/"$sample"/depth_of_coverage/ \ - --ntc_coverage "$output_path"/reanalysis/NTC-"$worksheet_id"/depth_of_coverage/ \ - --outfile "$output_path"/Gathered_Results/Database/"$sample"_"$referral"_coverage.json - - #Make new samplelist for upload - echo "${sample},${worksheet_id},DNA,$referral" > ${output_path}/Gathered_Results/Database/samples_database_${worksheet_id}_DNA_rereferral.csv -fi - -# deactivate env -set +u -conda deactivate -set -u diff --git a/scripts/call_extra_padding_variants.sh b/scripts/call_extra_padding_variants.sh deleted file mode 100644 index 6d3f0f2..0000000 --- a/scripts/call_extra_padding_variants.sh +++ /dev/null @@ -1,203 +0,0 @@ -#!/bin/bash - -# Illumina app only calls variants +/- 2bp of each exon, we require a larger area (usually +/- 5bp) -# Script re-runs part of illumina app to call variants between +/-2 to +/-5 - - -############################################################################################## -# Setup -############################################################################################## - -# get sample ID and pipeline version from sys args -sample_id=$1 -pipeline_version=$2 - -# define filepaths for app -app_version=2.2.0 -app_dir=/data/diagnostics/pipelines/TSO500/illumina_app/TSO500_RUO_LocalApp-"$app_version" - -# define filepaths for post processing -pipeline_dir=/data/diagnostics/pipelines/TSO500/TSO500_post_processing-"$pipeline_version" -pipeline_scripts="$pipeline_dir"/scripts - -cd "$SLURM_SUBMIT_DIR" - -# setup analysis folders and paths for singularity mounts -# folder for output of this script -output_folder="$SLURM_SUBMIT_DIR"/analysis/"$sample_id"/padding -mkdir -p $output_folder - -# mount path where data from first pass of Illumina app is stored -app_logs_intermediates="$SLURM_SUBMIT_DIR"/analysis/"$sample_id"/Logs_Intermediates - -# mount path for app resources folder -resources="$app_dir"/resources/ - -# load singularity and anaconda modules -module purge -module load singularity -. ~/.bashrc -module load anaconda -module load htslib - -# catch fails early and terminate -set -euo pipefail - -# define singularity exec command with folders mapped -SING="singularity exec --bind "$app_logs_intermediates":/mnt/app_result,"$output_folder":/opt/illumina/analysis-folder,"$resources":/opt/illumina/resources "$app_dir"/trusight-oncology-500-ruo.img" - -# path to updated ROI - this is only visible inside singularity container -extra_roi_bed_file=/opt/illumina/resources/TSO_extra_padding_chr.interval_list - - -############################################################################################## -# Re-run some app steps within singularity, output into output_folder variable above -# Most setting exactly the same but bed file switched for expanded ROI -############################################################################################## - -# re-run variant caller -$SING python /opt/illumina/step_modules/VariantCaller/variant_caller.py \ - --stepName VariantCaller \ - --dotnetPath dotnet \ - --outputFolder /opt/illumina/analysis-folder/Logs_Intermediates/VariantCaller \ - --dsdmFiles /mnt/app_result/Msi/dsdm.json \ - --inputBamFolder /mnt/app_result/StitchedRealigned \ - --inputMetricsFolder /mnt/app_result/CollapsedReads \ - --inputBamFileSuffix ".bam" \ - --outputVcfFileSuffix ".genome.vcf" \ - --outputFilteredFileSuffix ".filtered.genome.vcf" \ - --piscesPath "/opt/illumina/components/pisces/Pisces.dll" \ - --additionalPiscesArgs "-G /opt/illumina/resources/genomes/hg19_hardPAR -I "$extra_roi_bed_file" -MinVF 0.0001 -SSFilter False -MinMQ 30 -MaxVQ 100 -MinDepthFilter 500 -MinVQ 0 -VQFilter 20 -gVCF True -ReportNoCalls True -CallMNVs True -MaxMNVLength 3 -MaxGapBetweenMNV 1 -Collapse True -ReportRcCounts True -ReportTsCounts True -ThreadByChr True -usestitchedxd true -outputsbfiles false" \ - --psaraPath "/opt/illumina/components/psara/Psara.dll" \ - --additionalPsaraArgs "-roi "$extra_roi_bed_file" -inclusionmodel expand" - -# re-run small variant filter -$SING python "/opt/illumina/step_modules/SmallVariantFilter/small_variant_filter.py" \ - --stepName "SmallVariantFilter" \ - --outputFolder "/opt/illumina/analysis-folder/Logs_Intermediates/SmallVariantFilter" \ - --dsdmFiles "/opt/illumina/analysis-folder/Logs_Intermediates/VariantCaller/dsdm.json" \ - --inputFolder "/opt/illumina/analysis-folder/Logs_Intermediates/VariantCaller" \ - --inputFileSuffix ".filtered.genome.vcf" \ - --outputFileSuffix "_SmallVariants.genome.vcf" \ - --dotnetPath "dotnet"\ - --pepePath "/opt/illumina/components/Pepe/Pepe.dll" \ - --additionalPepeArgs "-genomeDirectory /opt/illumina/resources/genomes/hg19_hardPAR -blacklistBed /opt/illumina/resources/pepe2/pepe_blacklist.bed -baselineFile /opt/illumina/resources/pepe2/pepe_baseline.txt -mode likelihoodratio -depthThreshold 100 -baselineMethod binomial -priorFiles /opt/illumina/resources/pepe2/cosmic_pepe2_prior.vcf -likelihoodRatioNonPriorThreshold 60 -qscoreNonPriorThreshold 60 -qscorePriorThreshold 20 -likelihoodRatioPriorThreshold 20 -backgroundNoiseFrequencyThreshold 0.05 -LoD 0.05 -outputErrorRateTables true" - -# re-run phased variants -$SING dotnet /opt/illumina/step_modules/PhasedVariants/PhasedVariantsStepModule.dll \ - --stepName PhasedVariants \ - --componentPath /opt/illumina/components/scylla/Scylla.dll \ - --psaraPath /opt/illumina/components/psara/Psara.dll \ - --runtimePath dotnet \ - --inputBamFolder /mnt/app_result/StitchedRealigned \ - --inputBamFileSuffix .bam \ - --inputVcfFolder /opt/illumina/analysis-folder/Logs_Intermediates/SmallVariantFilter \ - --inputVcfFileSuffix _SmallVariants.genome.vcf \ - --dsdmFiles /opt/illumina/analysis-folder/Logs_Intermediates/SmallVariantFilter/dsdm.json \ - --outputFolder /opt/illumina/analysis-folder/Logs_Intermediates/PhasedVariants \ - --outputFileSuffix .Complex.vcf \ - --additionalComponentArgs '-g /opt/illumina/resources/genomes/hg19_hardPAR -PassingVariantsOnly false --minvq 0 --vqfilter 0 --vffilter 0 --gqfilter 0 --mindpfilter 100' \ - --additionalPsaraArgs '-inclusionmodel=start -roi /opt/illumina/resources/scylla/scylla.interval_list' - -# re-run variant matching -$SING dotnet /opt/illumina/step_modules/VariantMatching/VariantMatchingStepModule.dll \ - --stepName VariantMatching \ - --componentPath /opt/illumina/components/yente/Yente.dll \ - --runtimePath dotnet \ - --inputComplexVariantFolder /opt/illumina/analysis-folder/Logs_Intermediates/PhasedVariants \ - --inputComplexVariantFileSuffix .Complex.vcf \ - --inputComplexVariantWhitelistFile /opt/illumina/resources/yente/targeted_complex_variants_list.tsv \ - --inputSmallVariantFolder /opt/illumina/analysis-folder/Logs_Intermediates/SmallVariantFilter \ - --inputSmallVariantFileSuffix _SmallVariants.genome.vcf \ - --dsdmFiles /opt/illumina/analysis-folder/Logs_Intermediates/PhasedVariants/dsdm.json \ - --outputFolder /opt/illumina/analysis-folder/Logs_Intermediates/VariantMatching \ - --outputFileSuffix _MergedSmallVariants.genome.vcf - -# re-run contamination -$SING dotnet /opt/illumina/step_modules/Contamination/ContaminationStepModule.dll \ - --stepName "Contamination" \ - --outputFolder "/opt/illumina/analysis-folder/Logs_Intermediates/Contamination" \ - --spoilerPath "/opt/illumina/components/spoiler/Spoiler.dll" \ - --outputFileSuffix ".contamination.json" \ - --inputFileSuffix "_SmallVariants.genome.vcf" \ - --errorFileSuffix "_SmallVariants.genome.vcf.errorRates" \ - --runtimePath "dotnet" \ - --inputFolder "/opt/illumina/analysis-folder/Logs_Intermediates/SmallVariantFilter" \ - --dsdmFiles "/opt/illumina/analysis-folder/Logs_Intermediates/VariantMatching/dsdm.json" \ - --additionalSpoilerParameters "--vaf 0.25 --bedFile /opt/illumina/resources/contamination/Contamination.bed" \ - -# re-run annotation -$SING python /opt/illumina/step_modules/Annotation/annotation.py \ - --stepName Annotation \ - --outputFolder /opt/illumina/analysis-folder/Logs_Intermediates/Annotation \ - --nirvanaPath /opt/illumina/components/nirvana_3.2.3/Nirvana.dll \ - --additionalNirvanaArgs --disable-recomposition \ - --nirvanaCache /opt/illumina/resources/nirvana_3.2/Cache/26/GRCh37/Both \ - --nirvanaSupplement /opt/illumina/resources/nirvana_3.2/SupplementaryDatabase/3.2.0/GRCh37 \ - --nirvanaRef /opt/illumina/resources/nirvana_3.2/References/6/Homo_sapiens.GRCh37.Nirvana.dat \ - --outputFileSuffix _SmallVariants_Annotated.json.gz \ - --dotNetCorePath dotnet \ - --inputFileSuffix _SmallVariants.genome.vcf \ - --inputFolder /opt/illumina/analysis-folder/Logs_Intermediates/SmallVariantFilter \ - --dsdmFiles /opt/illumina/analysis-folder/Logs_Intermediates/Contamination/dsdm.json - -# re-run merged annotation -$SING python /opt/illumina/step_modules/Annotation/annotation.py \ - --stepName MergedAnnotation \ - --outputFolder /opt/illumina/analysis-folder/Logs_Intermediates/MergedAnnotation \ - --nirvanaPath /opt/illumina/components/nirvana_3.2.3/Nirvana.dll \ - --additionalNirvanaArgs --disable-recomposition \ - --nirvanaCache /opt/illumina/resources/nirvana_3.2/Cache/26/GRCh37/Both \ - --nirvanaSupplement /opt/illumina/resources/nirvana_3.2/SupplementaryDatabase/3.2.0/GRCh37 \ - --nirvanaRef /opt/illumina/resources/nirvana_3.2/References/6/Homo_sapiens.GRCh37.Nirvana.dat \ - --outputFileSuffix _MergedVariants_Annotated.json.gz \ - --dotNetCorePath dotnet \ - --inputFileSuffix _MergedSmallVariants.genome.vcf \ - --inputFolder /opt/illumina/analysis-folder/Logs_Intermediates/VariantMatching \ - --dsdmFiles /opt/illumina/analysis-folder/Logs_Intermediates/Annotation/dsdm.json - - -############################################################################################## -# Filter JSON output from nirvana into combined variant output file -############################################################################################## - -# activate conda env -set +u -conda activate TSO500_post_processing -set -u - -# unzip variant JSON -cp "$output_folder"/Logs_Intermediates/MergedAnnotation/"$sample_id"/"$sample_id"_MergedVariants_Annotated.json.gz "$output_folder" -gunzip "$output_folder"/"$sample_id"_MergedVariants_Annotated.json.gz - -# format extra variant calls with custom Python script -python "$pipeline_scripts"/filter_extra_padding_variants.py "$output_folder"/"$sample_id"_MergedVariants_Annotated.json > "$output_folder"/"$sample_id"_extra_db.tsv - -# add variants that have been blacklisted but we want to see -# vcf must be gzipped and tabix indexed -set +u -conda deactivate -conda activate pysam -set -u - -cp "$SLURM_SUBMIT_DIR"/analysis/"$sample_id"/Results/"$sample_id"/"$sample_id"_MergedSmallVariants.genome.vcf "$output_folder" -bgzip "$output_folder"/"$sample_id"_MergedSmallVariants.genome.vcf -tabix "$output_folder"/"$sample_id"_MergedSmallVariants.genome.vcf.gz -python "$pipeline_scripts"/keep_blacklisted_variants.py "$output_folder"/"$sample_id"_MergedSmallVariants.genome.vcf.gz >> "$output_folder"/"$sample_id"_extra_db.tsv - -set +u -conda deactivate -conda activate TSO500_post_processing -set -u - -# concatenate extra calls to end of combined output -cat "$SLURM_SUBMIT_DIR"/analysis/"$sample_id"/Results/"$sample_id"/"$sample_id"_CombinedVariantOutput.tsv > "$SLURM_SUBMIT_DIR"/analysis/"$sample_id"/Results/"$sample_id"/"$sample_id"_CombinedVariantOutput_padding.tsv -cat "$output_folder"/"$sample_id"_extra_db.tsv >> "$SLURM_SUBMIT_DIR"/analysis/"$sample_id"/Results/"$sample_id"/"$sample_id"_CombinedVariantOutput_padding.tsv - -# remove dsdm files to prevent Gathered results failing downstream - it uses a wildcard and they cause it to match too many folders -rm "$output_folder"/Logs_Intermediates/*/dsdm.json - -# deactivate env -set +u -conda deactivate -set -u diff --git a/scripts/coverage2json.py b/scripts/coverage2json.py deleted file mode 100755 index 6befde5..0000000 --- a/scripts/coverage2json.py +++ /dev/null @@ -1,541 +0,0 @@ -import json -import os -import argparse -import decimal -from decimal import Decimal - -import pandas as pd -import numpy as np - -""" -- script to format the output of CoverageCalculatorPy (.totalcoverage, .coverage) into a JSON format for importing into the new database -- for use as part of the TSO500 pipeline -- file requirements: - - for main gene regions: - - hotspot_coverage/_combined.groups - - NTC_coverage_results/__combined.totalCoverage - - sample_coverage_results/__combined.totalCoverage - - for hotspots: - - hotspot_coverage/_hotspots.bed - - NTC_coverage_results/__hotspots.coverage - - sample_coverage_results_270/__hotspots.coverage - - sample_coverage_results_135/__hotspots.coverage - - for genescreen: - - hotspot_coverage/_genescreen.bed - - NTC_coverage_results_270/__genescreen.coverage - - sample_coverage_results_270/__genescreen.coverage - - sample_coverage_results_135/__genescreen.coverage - - for gaps (hotspot only): - - sample_coverage_results_270/__hotspots.gaps - - sample_coverage_results_135/__hotspots.gaps -- usage: python coverage2json.py -r -g -s -n -o -- output: {sampleid}_{referral}_db_coverage.json file -{ - "gene1" : { - "average_depth" : , - "percent_135" : , - "percent_270" : , - "average_ntc" : , - "percent_ntc" : , - "genescreen_regions" : [ - [, , , "gene1", , <%@270>, <%@135>, , <%ntc>], - [, , , "gene1", , <%@270>, <%@135>, , <%ntc>] - ], - "hotspot_regions" : [ - [, , , "gene1", , <%@270>, <%@135>, , <%ntc>], - [, , , "gene1", , <%@270>, <%@135>, , <%ntc>] - ], - "gaps_135" : [], - "gaps_270" : [ - [, , , "gene1", ], - [, , , "gene1", ] - ] - } - "gene2" : { - "average_depth" : , - "percent_135" : , - "percent_270" : , - "average_ntc" : , - "percent_ntc" : , - "genescreen_regions" : [ - [, , , "gene2", , <%@270>, <%@135>, , <%ntc>], - [, , , "gene2", , <%@270>, <%@135>, , <%ntc>] - ], - "hotspot_regions" : [ - [, , , "gene2", , <%@270>, <%@135>, , <%ntc>], - [, , , "gene2", , <%@270>, <%@135>, , <%ntc>] - ], - "gaps_135" : [], - "gaps_270" : [ - [, , , "gene2", ], - [, , , "gene2", ] - ] - } - -} -""" - -##################################### -##### Functions ##### -##################################### - -def np_encoder(object): - """ - - function needed to allow json.dump to parse np values correctly - """ - if isinstance(object, np.generic): - return object.item() - - -def parse_referral_type_files(referral_type, groups_folder): - """ - - Function to parse referral type bed and group files - - input: referral type (eg: 'Thyroid'), pathway to hotspot_coverage folder containing the groups/bed files - - output: - 1) list of distinct gene names from _combined.groups file - 2) df of _genescreen.bed if present, blank if not present for referral type - 3) df of _hotspots.bed if present, blank if not present for referral type - 4) True or False value for if _genescreen.bed is present - 5) True or False value for if _hotspots.bed is present - """ - - ## create zero genescreen and hotspot counter - genescreen_count = 0 - hotspots_counter = 0 - - dir_list = os.listdir(groups_folder) - - for file in dir_list: - - filepath = os.path.join(groups_folder,file) - - ## parse groups file - if file == f'{referral_type}_combined.groups': - groups_df = pd.read_csv(filepath, sep = '\t', index_col = False) - gene_df = groups_df.drop_duplicates() - gene_list = gene_df['GENE'].values.tolist() - - ## parse genescreen.bed file - elif file == f'{referral_type}_genescreen.bed': - genescreen_count += 1 - genescreen_df = pd.read_csv(filepath, sep = '\t', names = ['CHR', 'START', 'END', 'INFO'], index_col = False) - genescreen_df.drop(columns = ['INFO'], inplace = True) - - ## parse hotspots.bed file - elif file == f'{referral_type}_hotspots.bed': - hotspots_counter += 1 - hotspots_df = pd.read_csv(filepath, sep = '\t', names = ['CHR', 'START', 'END', 'INFO'], index_col = False) - hotspots_df.drop(columns = ['INFO'], inplace = True) - - ## set genescreen variable as not all referral types have genescreen bed/groups - if genescreen_count > 0: - genescreen_present = True - - else: - genescreen_present = False - ## create blank dataframe to return when no genescreen .bed file present - genescreen_df = pd.DataFrame() - - ## set hotspots variable as not all referral types have hotspots bed/groups - if hotspots_counter > 0: - hotspots_present = True - - else: - hotspots_present = False - ## create blank dataframe to return when no hotspot .bed file present - hotspots_df = pd.DataFrame() - - - return gene_list, genescreen_df, hotspots_df, genescreen_present, hotspots_present - - -def parse_NTC_data(NTC_coverage_folder, referral_type, hotspots_present, genescreen_present): - """ - - function to parse NTC data from .totalCoverage and .coverage files from CoverageCalculatorPy - - input: path to NTC Coverage_results folder and referral type - - output: - 1) df of .totalcoverage gene level (gene id, ntc avg depth) - 2) df of .coverage hotspot region level (chr, start, end, meta, ntc avg depth) or blank df - 3) df of .coverage genescreen region level (chr, start, end, meta, ntc avg depth) or blank df - """ - - ## parse .totalCoverage and .coverage for NTC__combined - cov_filepath = os.path.join(NTC_coverage_folder,'hotspot_coverage_270x') - dir_list = os.listdir(cov_filepath) - - ## rip sampleid from filename - sampleid = dir_list[0].split('_')[0] - - for file in dir_list: - filepath = os.path.join(cov_filepath, file) - - ## parse .totalCoverage - if file == f'{sampleid}_{referral_type}_combined.totalCoverage': - ntc_gene_df = pd.read_csv(filepath, sep = '\t', index_col = False) - - ## drop final row in df as this is the total average across total panel - ntc_gene_df.drop(ntc_gene_df.tail(1).index, inplace = True) - - - ## get gene name positioning in 'feature' column (can change dependent on referral type) - feature_line = ntc_gene_df['FEATURE'][0].split('_') - gene_pos = len(feature_line) - 2 - - ## create 'gene' list and add to DF as a column - gene_list = [] - for line in ntc_gene_df['FEATURE']: - splitline = line.split('_') - ## if-loop to get around final row in the DF not containing gene name - if len(splitline) > gene_pos: - gene_list.append(splitline[gene_pos]) - else: - gene_list.append() - - ntc_gene_df.insert(0,'GENE', gene_list) - - ## drop irrelevant perc_coverage and feature column - ntc_gene_df.drop(columns = ['PERC_COVERAGE@270', 'FEATURE'], inplace = True) - - ntc_gene_df.rename(columns={'AVG_DEPTH':'NTC_AVG_DEPTH'}, inplace = True) - - ## parse .coverage for hotspots - elif file == f'{sampleid}_{referral_type}_hotspots.coverage': - ntc_hotspot_region_df = pd.read_csv(filepath, sep = '\t', index_col = False) - ntc_hotspot_region_df.drop(columns = ['PERC_COVERAGE@270'], inplace = True) - ntc_hotspot_region_df.rename(columns={'AVG_DEPTH':'NTC_AVG_DEPTH'}, inplace = True) - - - ## parse .coverage for genescreen - elif file == f'{sampleid}_{referral_type}_genescreen.coverage': - ntc_genescreen_region_df = pd.read_csv(filepath, sep = '\t', index_col = False) - ntc_genescreen_region_df.drop(columns = ['PERC_COVERAGE@270'], inplace = True) - ntc_genescreen_region_df.rename(columns={'AVG_DEPTH':'NTC_AVG_DEPTH'}, inplace = True) - - - ntc_gene_df['NTC_AVG_DEPTH'] = ntc_gene_df['NTC_AVG_DEPTH'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - - ## if hotspots present, format avg depth, or create empty df if not present - if hotspots_present: - ntc_hotspot_region_df['NTC_AVG_DEPTH'] = ntc_hotspot_region_df['NTC_AVG_DEPTH'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - else: - ntc_hotspot_region_df = pd.DataFrame() - - ## if genescreen present, format avg depth, or create empty df if not present - if genescreen_present: - ntc_genescreen_region_df['NTC_AVG_DEPTH'] = ntc_genescreen_region_df['NTC_AVG_DEPTH'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - else: - ntc_genescreen_region_df = pd.DataFrame() - - return ntc_gene_df, ntc_hotspot_region_df, ntc_genescreen_region_df - - -def parse_sample_data(sample_coverage_folder, referral_type, hotspots_present, genescreen_present): - """ - - function to parse sample data from .totalCoverage and .coverage files from CoverageCalculatorPy - - input: path to sample Coverage_results folder and referral type - - output: - 1) sampleid - 2) df of .totalcoverage gene level (gene id, avg depth, % cov 270, % cov 135) - 3) df of .coverage hotspot region level (chr, start, end, meta, avg depth, % cov 270, % cov 135) or blank df - 4) df of .coverage genescreen region level (chr, start, end, meta, avg depth, % cov 270, % cov 135) or blank df - 5) df of 135 .gaps (chr, start, end, meta, cosmic) - 6) df of 270 .gaps (chr, start, end, meta, cosmic) - """ - - ## parse 270x - cov_270_filepath = os.path.join(sample_coverage_folder,'hotspot_coverage_270x') - dir_list = os.listdir(cov_270_filepath) - - ## create gaps file counter - gaps_270_count = 0 - - ## rip sampleid from filename - sampleid = dir_list[0].split('_')[0] - - for file in dir_list: - filepath = os.path.join(cov_270_filepath, file) - - ## parse .totalCoverage for gene level info - if file == f'{sampleid}_{referral_type}_combined.totalCoverage': - sample_270_gene_df = pd.read_csv(filepath, sep = '\t', index_col = False) - - ## drop final row in df as this is the total average across total panel - sample_270_gene_df.drop(sample_270_gene_df.tail(1).index, inplace = True) - - ## get gene name positioning in 'feature' column (can change dependent on referral type) - feature_line = sample_270_gene_df['FEATURE'][0].split('_') - gene_pos = len(feature_line) - 2 - - ## create 'gene' list and add to DF as a column - gene_list = [] - for line in sample_270_gene_df['FEATURE']: - splitline = line.split('_') - ## if loop to get around final row in the DF not containing gene name - if len(splitline) > gene_pos: - gene_list.append(splitline[gene_pos]) - else: - gene_list.append() - - sample_270_gene_df.insert(0,'GENE', gene_list) - - ## drop irrelevant feature column - sample_270_gene_df.drop(columns = ['FEATURE'], inplace = True) - - ## parse .coverage for hotspots - elif file == f'{sampleid}_{referral_type}_hotspots.coverage': - sample_270_hotspot_region_df = pd.read_csv(filepath, sep = '\t', index_col = False) - - ## parse .coverage for genescreen - elif file == f'{sampleid}_{referral_type}_genescreen.coverage': - sample_270_genescreen_region_df = pd.read_csv(filepath, sep = '\t', index_col = False) - - ## parse 270 gaps (hotspot only) and add cosmic column - elif file == f'{sampleid}_{referral_type}_hotspots.gaps': - gaps_270_count += 1 - sample_270_gaps_df = pd.read_csv(filepath, sep = '\t', names = ['CHR', 'START', 'END', 'META'], header = None, index_col = False) - sample_270_gaps_df['COSMIC'] = 'N/A' - - - ## parse 135x - cov_135_filepath = os.path.join(sample_coverage_folder,'hotspot_coverage_135x') - dir_list = os.listdir(cov_135_filepath) - - ## create gaps file counter - gaps_135_count = 0 - - ## rip sampleid from filename - sampleid = dir_list[0].split('_')[0] - - for file in dir_list: - filepath = os.path.join(cov_135_filepath, file) - - ## parse .totalCoverage - if file == f'{sampleid}_{referral_type}_combined.totalCoverage': - sample_135_gene_df = pd.read_csv(filepath, sep = '\t', index_col = False) - - ## drop final row in df as this is the total average across total panel - sample_135_gene_df.drop(sample_135_gene_df.tail(1).index, inplace = True) - - ## get gene name positioning in 'feature' column (can change dependent on referral type) - feature_line = sample_135_gene_df['FEATURE'][0].split('_') - gene_pos = len(feature_line) - 2 - - ## create 'gene' list and add to DF as a column - gene_list = [] - for line in sample_135_gene_df['FEATURE']: - splitline = line.split('_') - gene_list.append(splitline[gene_pos]) - - sample_135_gene_df.insert(0,'GENE', gene_list) - - ## drop irrelevant feature column - sample_135_gene_df.drop(columns = ['FEATURE'], inplace = True) - - ## parse hotspot .coverage - elif file == f'{sampleid}_{referral_type}_hotspots.coverage': - sample_135_hotspot_region_df = pd.read_csv(filepath, sep = '\t', index_col = False) - - ## parse genescreen .coverage - elif file == f'{sampleid}_{referral_type}_genescreen.coverage': - sample_135_genescreen_region_df = pd.read_csv(filepath, sep = '\t', index_col = False) - - ## parse 135 gaps (hotspots only) - elif file == f'{sampleid}_{referral_type}_hotspots.gaps': - gaps_135_count += 1 - sample_135_gaps_df = pd.read_csv(filepath, sep = '\t', names = ['CHR', 'START', 'END', 'META'], header = None, index_col = False) - sample_135_gaps_df['COSMIC'] = 'N/A' - - - ## join 270 and 135 tables - ## join hotspots if present, remove nan values and round to integer, else make empty df - if hotspots_present: - sample_hotspot_region_df = pd.merge(sample_270_hotspot_region_df, sample_135_hotspot_region_df, how = 'outer', on = ['CHR', 'START', 'END', 'META', 'AVG_DEPTH']) - sample_hotspot_region_df['AVG_DEPTH'] = sample_hotspot_region_df['AVG_DEPTH'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - sample_hotspot_region_df['PERC_COVERAGE@270'] = sample_hotspot_region_df['PERC_COVERAGE@270'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - sample_hotspot_region_df['PERC_COVERAGE@135'] = sample_hotspot_region_df['PERC_COVERAGE@135'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - else: - sample_hotspot_region_df = pd.DataFrame() - - - ## join genescreen if present, remove nan values and round to integer, else make empty df - if genescreen_present: - sample_genescreen_region_df = pd.merge(sample_270_genescreen_region_df, sample_135_genescreen_region_df, how = 'outer', on = ['CHR', 'START', 'END', 'META', 'AVG_DEPTH']) - sample_genescreen_region_df['AVG_DEPTH'] = sample_genescreen_region_df['AVG_DEPTH'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - sample_genescreen_region_df['PERC_COVERAGE@270'] = sample_genescreen_region_df['PERC_COVERAGE@270'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - sample_genescreen_region_df['PERC_COVERAGE@135'] = sample_genescreen_region_df['PERC_COVERAGE@135'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - else: - sample_genescreen_region_df = pd.DataFrame() - - - ## join gene level - sample_gene_df = pd.merge(sample_270_gene_df, sample_135_gene_df, how = 'outer', on = ['GENE', 'AVG_DEPTH']) - sample_gene_df['AVG_DEPTH'] = sample_gene_df['AVG_DEPTH'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - sample_gene_df['PERC_COVERAGE@270'] = sample_gene_df['PERC_COVERAGE@270'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - sample_gene_df['PERC_COVERAGE@135'] = sample_gene_df['PERC_COVERAGE@135'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - - - ## make empty gaps df if no hotspots gaps files - if gaps_270_count == 0: - sample_270_gaps_df = pd.DataFrame(columns=['CHR', 'START', 'END', 'META', 'COSMIC']) - if gaps_135_count == 0: - sample_135_gaps_df = pd.DataFrame(columns=['CHR', 'START', 'END', 'META', 'COSMIC']) - - return sampleid, sample_gene_df, sample_hotspot_region_df, sample_genescreen_region_df, sample_135_gaps_df, sample_270_gaps_df - - -def create_output_dict(gene_list, main_gene_df, genescreen_region_df, hotspots_region_df, sample_270_gaps_df, sample_135_gaps_df, genescreen_present, hotspots_present): - ''' - - function to collate all dataframes into one nested dictionary to export to JSON format - - input: gene list, gene level df, genescreen region df, hotspot region df, 270 gaps df, 135 gaps df - - output: dictionary formatted as JSON specified at top of script - ''' - - output_dict = {} - for gene in gene_list: - output_dict[gene] = {} - - for key in output_dict.keys(): - output_dict[key]['average_depth'] = main_gene_df.at[key, 'AVG_DEPTH'] - output_dict[key]['percent_135'] = main_gene_df.at[key, 'PERC_COVERAGE@135'] - output_dict[key]['percent_270'] = main_gene_df.at[key, 'PERC_COVERAGE@270'] - output_dict[key]['average_ntc'] = main_gene_df.at[key, 'NTC_AVG_DEPTH'] - output_dict[key]['percent_ntc'] = main_gene_df.at[key, 'PERC_NTC_DEPTH'] - - ## genescreen - if genescreen_present: - filtered_genescreen_region_list =[] - genescreen_region_list = genescreen_region_df.values.tolist() - for item in genescreen_region_list: - # check if gene is the gene in the 4th column then add - if key == item[3].split('(')[0]: - filtered_genescreen_region_list.append(item) - output_dict[key]['genescreen_regions'] = filtered_genescreen_region_list - else: - output_dict[key]['genescreen_regions'] = [] - - ## hotspots - if hotspots_present: - filtered_hotspot_region_list = [] - hotspot_region_list = hotspots_region_df.values.tolist() - for item in hotspot_region_list: - # check if gene is the gene in the 4th column then add - if key == item[3].split('(')[0]: - filtered_hotspot_region_list.append(item) - - output_dict[key]['hotspot_regions'] = filtered_hotspot_region_list - - ## check if any gaps and add if there are - if len(sample_135_gaps_df) > 0: - filtered_135_gaps_list = [] - sample_135_gaps_list = sample_135_gaps_df.values.tolist() - for item in sample_135_gaps_list: - # bed2hgvs doesnt work for POLE - if key == 'POLE': - hgvs_c = item[3].split(':')[1] - filtered_135_gaps_list.append([item[0], item[1], item[2], f'POLE(NM_006231.3):{hgvs_c}', item[4]]) - - # check if gene is the gene in the 4th column then add - if key == item[3].split('(')[0]: - filtered_135_gaps_list.append(item) - - output_dict[key]['gaps_135'] = filtered_135_gaps_list - else: - output_dict[key]['gaps_135'] = [] - - if len(sample_270_gaps_df) > 0: - filtered_270_gaps_list = [] - sample_270_gaps_list = sample_270_gaps_df.values.tolist() - for item in sample_270_gaps_list: - # bed2hgvs doesnt work for POLE - if key == 'POLE': - hgvs_c = item[3].split(':')[1] - filtered_270_gaps_list.append([item[0], item[1], item[2], f'POLE(NM_006231.3):{hgvs_c}', item[4]]) - - # check if gene is the gene in the 4th column then add - if key == item[3].split('(')[0]: - filtered_270_gaps_list.append(item) - - output_dict[key]['gaps_270'] = filtered_270_gaps_list - else: - output_dict[key]['gaps_270'] = [] - - - else: - output_dict[key]['hotspot_regions'] = [] - output_dict[key]['gaps_135'] = [] - output_dict[key]['gaps_270'] = [] - - - return output_dict - - - -######################################### -##### Programme ##### -######################################### - - -if __name__ == '__main__': - - - ## args - parser = argparse.ArgumentParser() - parser.add_argument('--referral','-r', help = 'Referral type. eg: Thyroid') - parser.add_argument('--groups_folder','-g', help = 'pathway to hotspots_coverage folder') - parser.add_argument('--ntc_coverage','-n', help = 'pathway to NTC Coverage_results folder') - parser.add_argument('--sample_coverage','-s', help = 'pathway to sample Coverage_results folder') - parser.add_argument('--outfile', '-o', help = 'pathway/file of output') - args = parser.parse_args() - - - ## set decimal settings - decimal.getcontext().rounding = decimal.ROUND_DOWN - - - ### parse referral_type group/bed files - gene_list, genescreen_df, hotspots_df, genescreen_present, hotspots_present = parse_referral_type_files(args.referral, args.groups_folder) - - ### parse NTC sample 270x for average depth per gene (.totalCoverage) and per region (.coverage) - ntc_gene_df, ntc_hotspot_region_df, ntc_genescreen_region_df = parse_NTC_data(args.ntc_coverage, args.referral, hotspots_present, genescreen_present) - - - ### parse sample 135x and 270x files - sampleid, sample_gene_df, sample_hotspot_region_df, sample_genescreen_region_df, sample_135_gaps_df, sample_270_gaps_df = parse_sample_data(args.sample_coverage, args.referral, hotspots_present, genescreen_present) - - ### create json pieces - ## join NTC data to hotspots and genescreen dfs if present, else create blank df - if hotspots_present: - main_hotspot_region_df = pd.merge(sample_hotspot_region_df, ntc_hotspot_region_df, how = 'outer', on = ['CHR', 'START', 'END', 'META']) - main_hotspot_region_df['PERC_NTC_DEPTH'] = (main_hotspot_region_df['NTC_AVG_DEPTH'] / main_hotspot_region_df['AVG_DEPTH']) * 100 - main_hotspot_region_df['PERC_NTC_DEPTH'] = main_hotspot_region_df['PERC_NTC_DEPTH'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - else: - main_hotspot_region_df = pd.DataFrame() - - if genescreen_present: - main_genescreen_region_df = pd.merge(sample_genescreen_region_df, ntc_genescreen_region_df, how = 'outer', on = ['CHR', 'START', 'END', 'META']) - main_genescreen_region_df['PERC_NTC_DEPTH'] = (main_genescreen_region_df['NTC_AVG_DEPTH'] / main_genescreen_region_df['AVG_DEPTH']) * 100 - main_genescreen_region_df['PERC_NTC_DEPTH'] = main_genescreen_region_df['PERC_NTC_DEPTH'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - else: - main_genescreen_region_df = pd.DataFrame() - - ## join ntc information to gene level df - main_gene_df = pd.merge(sample_gene_df, ntc_gene_df, how = 'outer', on = ['GENE']) - - - ## change index of gene df to be the gene name for iloc later - main_gene_df.set_index('GENE', inplace = True) - - - ## create and format percent NTC column - main_gene_df['PERC_NTC_DEPTH'] = (main_gene_df['NTC_AVG_DEPTH'] / main_gene_df['AVG_DEPTH']) * 100 - main_gene_df['PERC_NTC_DEPTH'] = main_gene_df['PERC_NTC_DEPTH'].apply(lambda x: None if np.isnan(x) else int((Decimal(str(x)).quantize(Decimal('1'))))) - - - ### create output dict - output_dict = create_output_dict(gene_list, main_gene_df, main_genescreen_region_df, main_hotspot_region_df, sample_270_gaps_df, sample_135_gaps_df, genescreen_present, hotspots_present) - - ## export dict to JSON - with open(args.outfile,'w') as f: - json.dump(output_dict, f, indent = 4, default = np_encoder) - - diff --git a/scripts/filter_extra_padding_variants.py b/scripts/filter_extra_padding_variants.py deleted file mode 100644 index da31bf6..0000000 --- a/scripts/filter_extra_padding_variants.py +++ /dev/null @@ -1,88 +0,0 @@ -""" -filter JSON from nirvana output produced in call_extra_variants.sh. -Outputs variants formatted so that they can be appended onto the bottom of the -main CombinedVariantReport file from the app - -""" - -import sys -import json - -# open annotated variants JSON passed in as sys arg -with open(sys.argv[1], 'r') as f: - y = json.load(f) - -# make empty list for results output -out_list = [] - -# loop through each variant and pull out info if the filter is pass (based on structure of JSON) -for var in y['positions']: - if 'PASS' in var['filters']: - - # info common to variant (regardless of transcript) - chr = var['chromosome'] - pos = str(var['position']) - ref = var['refAllele'] - - vaf = var['samples'][0]['variantFrequencies'][0] - depth = var['samples'][0]['totalDepth'] - alt_reads = int(vaf * depth) - - # could be multiallelic so loop through each variant option - for variant in var['variants']: - - alt = variant['altAllele'] - - # transcript specific info - use canonical refseq - for transcript in variant['transcripts']: - - # variable to decide whether or not to keep a variant - keep = False - - # weird transcripts - if transcript['transcript'] in ['NM_000141.4', 'NM_000142.4', 'NM_153759.3', 'NM_001122607.1']: - keep = True - - # padding variants - if transcript['source'] == 'RefSeq' and 'isCanonical' in transcript.keys(): - if transcript['isCanonical']: - keep = True - - # output any variants to keep into the output list - if keep: - # keys are only present in JSON if they're not empty - if 'hgnc' in transcript.keys(): - gene = transcript['hgnc'] - else: - gene = '' - - if 'hgvsp' in transcript.keys(): - hgvs_p = transcript['hgvsp'] - else: - hgvs_p = '' - - if 'hgvsc' in transcript.keys(): - hgvs_c = transcript['hgvsc'] - else: - hgvs_c = '' - - if 'consequence' in transcript.keys(): - csq = ':'.join(transcript['consequence']) - else: - csq = '' - - if 'exon' in transcript.keys(): - exon = transcript['exon'] - else: - exon = '' - - # add to variant list - out_list.append( - [gene, chr, pos, ref, alt, str(vaf), str(depth), hgvs_p, hgvs_c, csq, exon] - ) - - - -# print to screen - redirect to output within pipeline -for var in out_list: - print('\t'.join(var)) diff --git a/scripts/gather_list.py b/scripts/gather_list.py deleted file mode 100755 index 2fbf325..0000000 --- a/scripts/gather_list.py +++ /dev/null @@ -1,23 +0,0 @@ -""" -Prints a specifically formatted list of samples for input to the Illumina app. -Must start with the Demultiplex_Output folder and all folders must have the full file path - -""" -import os -import sys - -# load in system arguments -in_file = sys.argv[1] -wd = sys.argv[2] - -# list must start with Demultiplex_Output folder -gather_list = [f'{wd}/Demultiplex_Output'] - -# add each sample analysis folder to the end of the list -with open(in_file, 'r') as file: - for line in file: - sample = line.split(",")[0] - gather_list.append(f'{wd}/analysis/{sample}\n') - -# print the whole list seperated by spaces -print(' '.join(gather_list)) diff --git a/scripts/keep_blacklisted_variants.py b/scripts/keep_blacklisted_variants.py deleted file mode 100644 index 5cf8ece..0000000 --- a/scripts/keep_blacklisted_variants.py +++ /dev/null @@ -1,106 +0,0 @@ -import sys -from pysam import VariantFile -import decimal - -# set decimal to always round down -decimal.getcontext().rounding = decimal.ROUND_HALF_DOWN - -# load in VCF and make pysam object. Must be gzipped and tabix indexed -input_vcf = sys.argv[1] -vcf = VariantFile(input_vcf) - -# list to store output -output_list = [] - -# list of the variants that we want to ignore the blacklist on, plus associated annotations -# Add to this list if any more variants need removing from the blacklist -variants_to_keep = [ - { - 'chr': 'chr20', - 'pos': 31022441, - 'gene': 'ASXL1', - 'ref': 'A', - 'alt': 'AG', - 'hgvs_c': 'NM_015338.5:c.1934dup', - 'hgvs_p': 'NP_056153.2:p.(Gly646TrpfsTer12)', - 'csq': 'frameshift_variant', - 'exon': '13/17', - 'cutoff': 0.1, - }, - { - 'chr': 'chr10', - 'pos': 89720653, - 'gene': 'PTEN', - 'ref': 'C', - 'alt': 'CA', - 'hgvs_c': 'NM_000314.6:c.808dup', - 'hgvs_p': 'NP_000305.3:p.(Met270AsnfsTer28)', - 'csq': 'frameshift_variant', - 'exon': '8/9', - 'cutoff': 0, - }, - { - 'chr': 'chr10', - 'pos': 89720679, - 'gene': 'PTEN', - 'ref': 'C', - 'alt': 'T', - 'hgvs_c': 'NM_000314.6:c.830C>T', - 'hgvs_p': 'NP_000305.3:p.(Thr277Ile)', - 'csq': 'missense_variant', - 'exon': '8/9', - 'cutoff': 0, - }, -] - -# search VCF for each of the variants we'd like to keep -for var in variants_to_keep: - - # loop through all variants at the position (might be multiple as each alt has a new line) - for rec in vcf.fetch(var['chr'], var['pos'] -1, var['pos']): - - # get all filters for variant - filters = rec.filter.keys() - - # remove blacklist from filters list - if 'Blacklist' in filters: - filters.remove('Blacklist') - - # if no more filters (i.e. blacklist was the only filter), then add variant to report - if len(filters) == 0: - - # only pull through specific base changes - if var['ref'] == rec.ref and var['alt'] == rec.alts[0]: - base_changes_pass = True - else: - base_changes_pass = False - - # pull out VAF, make decimal and round to 4dp - vaf = decimal.Decimal(rec.samples[0]['VF'][0]).quantize(decimal.Decimal('0.0001')) - - # some should only be pulled through above a certain VAF, defined in config above. If no cutoff then config will be 0 - if vaf > var['cutoff']: - vaf_pass = True - else: - vaf_pass = False - - # if both filters pass then add to output - if vaf_pass and base_changes_pass: - - output_list.append([ - var['gene'], - rec.chrom, - str(rec.pos), - rec.ref, - rec.alts[0], - str(vaf), - str(rec.samples[0]['DP']), - var['hgvs_p'], - var['hgvs_c'], - var['csq'], - var['exon'], - ]) - -# print to screen - redirect to output within pipeline -for var in output_list: - print('\t'.join(var)) diff --git a/scripts/tsv2db.py b/scripts/tsv2db.py deleted file mode 100755 index 220753c..0000000 --- a/scripts/tsv2db.py +++ /dev/null @@ -1,163 +0,0 @@ -import argparse -import decimal -from decimal import Decimal - -""" -- script to format small variants part of variant.tsv files from the illumina localapp output to new database friendly format -- For use as part of TSO500 pipeline -- usage: python tsv2db.py -t -n -o -- output: tab delimited table with columns: gene, chr, pos, ref, alt, vaf, depth, hgvs_p, hgvs_c, consequence, exon, alt_reads, in_ntc, ntc_vaf, ntc_depth, ntc_alt_reads -""" - - -############################### -### Functions ### -############################### - -def parse_ntc_tsv(ntcfile): - """ - - returns a list of list of variant information (chr, start, end, meta, vaf, depth) for ntc or ['NA'] if no variants found - """ - - ## create base variables - start_parsing = False - rowcounter = 0 - ntc_var_list = [] - - tsv = open(ntcfile, 'r') - for tsv_line in tsv: - - ## look for dataset_title before starting to parse the subsequent lines - if start_parsing == False: - if tsv_line.startswith('[Small Variants]'): - start_parsing = True - pass - - else: - pass - - else: - ## treat first line differently as it is a header line - if rowcounter == 0: - rowcounter += 1 - - else: - tsv_line_list = tsv_line.rstrip().split('\t') - if len(tsv_line_list) > 6: - var_id = tsv_line_list[0:7] - ntc_var_list.append(var_id) - - tsv.close() - - return ntc_var_list - - -def parse_sample_tsv(tsvfile, ntcvarlist): - """ - - returns a list of variant informaiton for sample in format: - 'gene', 'chr', 'pos', 'ref', 'alt', 'vaf', 'depth', 'hgvs_p', 'hgvs_c', 'consequence', 'exon', 'alt_reads', 'in_ntc', 'ntc_vaf', 'ntc_depth'. 'ntc_alt_reads' - - ntc_vaf and ntc_depth are only populated if in_ntc = TRUE - """ - - ## create base variables - start_parsing = False - rowcounter = 0 - var_list = [] - - sampletsv = open(tsvfile, 'r') - for tsv_line in sampletsv: - - ## look for dataset_title before starting to parse the subsequent lines - if start_parsing == False: - if tsv_line.startswith('[Small Variants]'): - start_parsing = True - pass - - else: - pass - else: - - ## treat first line differently as it is a header line - if rowcounter == 0: - rowcounter += 1 - - else: - - ## parse small variants data - tsv_line1 = tsv_line.replace('\n','') - tsv_line_list = tsv_line1.rstrip().split('\t') - - ## check if variant is in NTC file - var_id_list = tsv_line_list[0:5] - in_ntc_count = 0 - - for item in ntcvarlist: - - ## if var is in ntc var, create counter and then - if item[0:5] == var_id_list: - in_ntc_count += 1 - ntc_vaf = item[5] - ntc_depth = item[6] - ntc_allele_percent = float(ntc_vaf) * 100 - ntc_alt_reads = (int(ntc_depth) / 100) * ntc_allele_percent - ntc_alt_reads_rounded = int((Decimal(str(ntc_alt_reads)).quantize(Decimal('1')))) - - ## if in ntc, then give out ntc vaf, depth, and alt read count - if in_ntc_count > 0: - in_ntc = f'True\t{ntc_vaf}\t{ntc_depth}\t{ntc_alt_reads_rounded}' - - else: - in_ntc = 'False' - - ## get alt_reads - ## special case to exclude blank lines at end of tsv - if len(tsv_line_list) > 5: - allele_percent = float(tsv_line_list[5]) * 100 - alt_reads = (int(tsv_line_list[6]) / 100) * allele_percent - alt_reads_rounded = int((Decimal(str(alt_reads)).quantize(Decimal('1')))) - - ## append info in correct order - var_info = f'{tsv_line1}\t{alt_reads_rounded}\t{in_ntc}' - - ## add line list into main list for exporting later - var_list.append(var_info) - sampletsv.close() - - return var_list - - -############################### -### Programme ### -############################### - - -if __name__ == '__main__': - - ## args - parser = argparse.ArgumentParser() - parser.add_argument('--tsvfile','-t', help = 'pathway to tsv combined variants file') - parser.add_argument('--ntcfile','-n', help = 'pathway to NTC tsv combined variants file') - parser.add_argument('--outfile','-o', help = 'filename/path for output') - args = parser.parse_args() - - ## set Decimal settings - decimal.getcontext().rounding = decimal.ROUND_HALF_UP - - ### parse NTC file - ntc_var_list = parse_ntc_tsv(args.ntcfile) - - ### parse sample file - var_list = parse_sample_tsv(args.tsvfile, ntc_var_list) - - - ### export data - ## create header line - outfile_headers = ['gene', 'chr', 'pos', 'ref', 'alt', 'vaf', 'depth', 'hgvs_p', 'hgvs_c', 'consequence', 'exon', 'alt_reads', 'in_ntc', 'ntc_vaf', 'ntc_depth', 'ntc_alt_reads'] - outfile_headers_string = '\t'.join(outfile_headers) - - ## export information to file - with open(args.outfile,'w',newline='') as file: - file.write(outfile_headers_string + '\n') - - for line in var_list: - file.write(line + '\n') diff --git a/tests/test_data_tsv2db/NTC_fake_variants.tsv b/tests/test_data_tsv2db/NTC_fake_variants.tsv deleted file mode 100755 index ded1db1..0000000 --- a/tests/test_data_tsv2db/NTC_fake_variants.tsv +++ /dev/null @@ -1,43 +0,0 @@ -TruSight Oncology 500 - Combined Variant Output -For Research Use Only. Not for use in diagnostic procedures. - -[Analysis Details] -Pair ID NTC-DNA-1 -DNA Sample ID NTC-DNA-1 -RNA Sample ID NA -Output Date 2099-99-99 -Output Time 14:24:32 -Module Version NA -Pipeline Version 1 - -[Sequencing Run Details] -NA - -[TMB] -Total TMB NA -Coding Region Size in Megabases NA -Number of Passing Eligible Variants NA - -[MSI] -Usable MSI Sites 0 -Total MSI Sites Unstable NA -Percent Unstable MSI Sites NA - -[Gene Amplifications] -Gene Fold Change -NA - -[Splice Variants] -Gene Affected Exon Breakpoint 1 Breakpoint 2 Splice Supporting Reads Reference Reads Transcript -NA - -[Fusions] -Gene Pair Breakpoint 1 Breakpoint 2 Fusion Supporting Reads Gene 1 Reference Reads Gene 2 Reference Reads -NA - -[Small Variants] -Gene Chromosome Genomic Position Reference Call Alternative Call Allele Frequency Depth P-Dot Notation C-Dot Notation Consequence(s) Affected Exon(s) -TNFRSF14 chr1 2489805 G A 0.0936 87 NP_003811.2:p.(Gly68Arg) NM_003820.3:c.202G>A missense_variant 3/8 -MTOR chr1 11288758 G A 0.7032 873 NM_004958.3:c.2997C>T(p.(Asn999=)) NM_004958.3:c.2997C>T synonymous_variant 19/58 -MTOR chr1 11301744 A G 0.6751 12 NM_004958.3:c.1437T>C(p.(Asp479=)) NM_004958.3:c.1437T>C synonymous_variant 10/58 - chr9 19072413 C T 0.1033 400 diff --git a/tests/test_data_tsv2db/NTC_no_var.tsv b/tests/test_data_tsv2db/NTC_no_var.tsv deleted file mode 100755 index b036b58..0000000 --- a/tests/test_data_tsv2db/NTC_no_var.tsv +++ /dev/null @@ -1,40 +0,0 @@ -TruSight Oncology 500 - Combined Variant Output -For Research Use Only. Not for use in diagnostic procedures. - -[Analysis Details] -Pair ID NTC-DNA-1 -DNA Sample ID NTC-DNA-1 -RNA Sample ID NA -Output Date 2099-99-99 -Output Time 14:24:32 -Module Version NA -Pipeline Version 1 - -[Sequencing Run Details] -NA - -[TMB] -Total TMB NA -Coding Region Size in Megabases NA -Number of Passing Eligible Variants NA - -[MSI] -Usable MSI Sites 0 -Total MSI Sites Unstable NA -Percent Unstable MSI Sites NA - -[Gene Amplifications] -Gene Fold Change -NA - -[Splice Variants] -Gene Affected Exon Breakpoint 1 Breakpoint 2 Splice Supporting Reads Reference Reads Transcript -NA - -[Fusions] -Gene Pair Breakpoint 1 Breakpoint 2 Fusion Supporting Reads Gene 1 Reference Reads Gene 2 Reference Reads -NA - -[Small Variants] -Gene Chromosome Genomic Position Reference Call Alternative Call Allele Frequency Depth P-Dot Notation C-Dot Notation Consequence(s) Affected Exon(s) -NA diff --git a/tests/test_data_tsv2db/NTC_novar_blanks.tsv b/tests/test_data_tsv2db/NTC_novar_blanks.tsv deleted file mode 100755 index 150aa05..0000000 --- a/tests/test_data_tsv2db/NTC_novar_blanks.tsv +++ /dev/null @@ -1,44 +0,0 @@ -TruSight Oncology 500 - Combined Variant Output -For Research Use Only. Not for use in diagnostic procedures. - -[Analysis Details] -Pair ID NTC-DNA-1 -DNA Sample ID NTC-DNA-1 -RNA Sample ID NA -Output Date 2099-99-99 -Output Time 14:24:32 -Module Version NA -Pipeline Version 1 - -[Sequencing Run Details] -NA - -[TMB] -Total TMB NA -Coding Region Size in Megabases NA -Number of Passing Eligible Variants NA - -[MSI] -Usable MSI Sites 0 -Total MSI Sites Unstable NA -Percent Unstable MSI Sites NA - -[Gene Amplifications] -Gene Fold Change -NA - -[Splice Variants] -Gene Affected Exon Breakpoint 1 Breakpoint 2 Splice Supporting Reads Reference Reads Transcript -NA - -[Fusions] -Gene Pair Breakpoint 1 Breakpoint 2 Fusion Supporting Reads Gene 1 Reference Reads Gene 2 Reference Reads -NA - -[Small Variants] -Gene Chromosome Genomic Position Reference Call Alternative Call Allele Frequency Depth P-Dot Notation C-Dot Notation Consequence(s) Affected Exon(s) -NA - - - - diff --git a/tests/test_data_tsv2db/sample_CombinedVariantOutput.tsv b/tests/test_data_tsv2db/sample_CombinedVariantOutput.tsv deleted file mode 100755 index 4d6cd47..0000000 --- a/tests/test_data_tsv2db/sample_CombinedVariantOutput.tsv +++ /dev/null @@ -1,76 +0,0 @@ -TruSight Oncology 500 - Combined Variant Output -For Research Use Only. Not for use in diagnostic procedures. - -[Analysis Details] -Pair ID 12345 -DNA Sample ID 12345 -RNA Sample ID NA -Output Date 2099-99-99 -Output Time 18:33:23 -Module Version NA -Pipeline Version 1 - -[Sequencing Run Details] -NA - -[TMB] -Total TMB 275.6 -Coding Region Size in Megabases 1.28 -Number of Passing Eligible Variants 352 - -[MSI] -Usable MSI Sites 125 -Total MSI Sites Unstable 81 -Percent Unstable MSI Sites 64.8 - -[Gene Amplifications] -Gene Fold Change -MYCN 4.464 -MET 2.173 -MYC 4.76 - -[Splice Variants] -Gene Affected Exon Breakpoint 1 Breakpoint 2 Splice Supporting Reads Reference Reads Transcript -NA - -[Fusions] -Gene Pair Breakpoint 1 Breakpoint 2 Fusion Supporting Reads Gene 1 Reference Reads Gene 2 Reference Reads -NA - -[Small Variants] -Gene Chromosome Genomic Position Reference Call Alternative Call Allele Frequency Depth P-Dot Notation C-Dot Notation Consequence(s) Affected Exon(s) -TNFRSF14 chr1 2488153 A G 0.3967 910 NP_003811.2:p.(Lys17Arg) NM_003820.3:c.50A>G missense_variant 1/8 -TNFRSF14 chr1 2489805 G A 0.0936 1240 NP_003811.2:p.(Gly68Arg) NM_003820.3:c.202G>A missense_variant 3/8 -MTOR chr1 11174511 C A 0.0467 899 NM_004958.3:c.7165-1G>T splice_acceptor_variant -MTOR chr1 11288758 G A 0.7032 1388 NM_004958.3:c.2997C>T(p.(Asn999=)) NM_004958.3:c.2997C>T synonymous_variant 19/58 -MTOR chr1 11301714 A G 0.6751 1225 NM_004958.3:c.1437T>C(p.(Asp479=)) NM_004958.3:c.1437T>C synonymous_variant 10/58 -SPEN chr1 16255108 A G 0.0996 1185 NM_015001.2:c.2373A>G(p.(Thr791=)) NM_015001.2:c.2373A>G synonymous_variant 11/15 -SPEN chr1 16255644 C T 0.2316 1321 NP_055816.2:p.(Ala970Val) NM_015001.2:c.2909C>T missense_variant 11/15 - chr9 19072413 C T 0.1033 1404 -FGF14 chr13 102382362 C A 0.429 1112 NM_175929.2:c.424-3202G>T intron_variant -FGF14 chr13 102589909 C T 0.1469 1055 NM_175929.2:c.209-62263G>A intron_variant -ERCC5 chr13 103528002 G C 0.3986 1119 NP_000114.2:p.(Asp1104His) NM_000123.3:c.3310G>C missense_variant 15/15 -IRS2 chr13 110435914 G A 0.0518 791 NM_003749.2:c.2487C>T(p.(Pro829=)) NM_003749.2:c.2487C>T synonymous_variant 1/2 -IRS2 chr13 110435953 A G 0.6511 963 NM_003749.2:c.2448T>C(p.(Cys816=)) NM_003749.2:c.2448T>C synonymous_variant 1/2 -IRS2 chr13 110436232 G A 0.6667 402 NM_003749.2:c.2169C>T(p.(Ser723=)) NM_003749.2:c.2169C>T synonymous_variant 1/2 -NFKBIA chr14 35872926 G A 0.0311 1352 NM_020529.2:c.306C>T(p.(Ala102=)) NM_020529.2:c.306C>T synonymous_variant 2/6 -NFKBIA chr14 35873770 G A 0.1058 1106 NM_020529.2:c.81C>T(p.(Asp27=)) NM_020529.2:c.81C>T synonymous_variant 1/6 -NKX2-1 chr14 36986656 C A 0.1068 103 NP_001073136.1:p.(Ala345Ser) NM_001079668.2:c.1033G>T missense_variant 3/3 -NKX2-1 chr14 36991098 C G 0.0682 1525 upstream_gene_variant -FGF7 chr15 49756480 G T 0.1051 1151 NM_002009.3:c.287-18868G>T intron_variant -MAPK3 chr16 30134375 C T 0.0325 738 NM_002746.2:c.156G>A(p.(Ala52=)) NM_002746.2:c.156G>A synonymous_variant 1/9 -PRSS8 chr16 31144657 G A 0.0993 1359 NM_002773.3:c.156C>T(p.(Val52=)) NM_002773.3:c.156C>T synonymous_variant 3/6 -CYLD chr16 50827518 C T 0.1381 1072 NM_015247.2:c.2412C>T(p.(Asp804=)) NM_015247.2:c.2412C>T synonymous_variant 18/20 -AKT2 chr19 40736295 G T 0.0366 1258 NM_001626.5:c.*3484C>A 3_prime_UTR_variant 14/14 -AKT2 chr19 40737242 T C 1 1390 NM_001626.5:c.*2537= 3_prime_UTR_variant 14/14 -ARFRP1 chr20 62331839 C T 0.0409 1198 NP_003215.1:p.(Val188Met) NM_003224.5:c.562G>A missense_variant 8/8 -ARFRP1 chr20 62331989 T G 0.2329 1065 NM_003224.5:c.483A>C(p.(Arg161=)) NM_003224.5:c.483A>C synonymous_variant 7/8 -ARFRP1 chr20 62333536 T C 0.0739 1353 NP_003215.1:p.(Ile100Val) NM_003224.5:c.298A>G missense_variant 5/8 -EP300 chr22 41566447 G T 0.0645 1024 NP_001420.2:p.(Glu1442Ter) NM_001429.3:c.4324G>T stop_gained 27/31 -EP300 chr22 41566524 CA C 0.1877 554 NP_001420.2:p.(Met1470CysfsTer26) NM_001429.3:c.4408del frameshift_variant 27/31 -EP300 chr22 41568524 G A 0.046 630 NP_001420.2:p.(Glu1492Lys) NM_001429.3:c.4474G>A missense_variant 28/31 -EP300 chr22 41568531 G A 0.0433 693 NP_001420.2:p.(Arg1494Lys) NM_001429.3:c.4481G>A missense_variant 28/31 -KDM6A chrX 44929077 C A 0.1299 1032 NP_001278344.1:p.(Thr778Lys) NM_001291415.1:c.2333C>A missense_variant 18/30 -KDM6A chrX 44938563 G A 0.4155 722 NM_001291415.1:c.3267G>A(p.(Gln1089=)) NM_001291415.1:c.3267G>A synonymous_variant 21/30 -RBM10 chrX 47041246 G A 0.0541 1073 NM_001204468.1:c.1869G>A(p.(Gln623=)) NM_001204468.1:c.1869G>A synonymous_variant 15/24 -RBM10 chrX 47045888 C T 0.0687 728 NP_001191397.1:p.(Arg960Trp) NM_001204468.1:c.2878C>T missense_variant 24/24 diff --git a/tests/test_data_tsv2db/sample_CombinedVariantOutput_blanks.tsv b/tests/test_data_tsv2db/sample_CombinedVariantOutput_blanks.tsv deleted file mode 100755 index 1d58e30..0000000 --- a/tests/test_data_tsv2db/sample_CombinedVariantOutput_blanks.tsv +++ /dev/null @@ -1,78 +0,0 @@ -TruSight Oncology 500 - Combined Variant Output -For Research Use Only. Not for use in diagnostic procedures. - -[Analysis Details] -Pair ID 12345 -DNA Sample ID 12345 -RNA Sample ID NA -Output Date 2099-99-99 -Output Time 18:33:23 -Module Version NA -Pipeline Version 1 - -[Sequencing Run Details] -NA - -[TMB] -Total TMB 275.6 -Coding Region Size in Megabases 1.28 -Number of Passing Eligible Variants 352 - -[MSI] -Usable MSI Sites 125 -Total MSI Sites Unstable 81 -Percent Unstable MSI Sites 64.8 - -[Gene Amplifications] -Gene Fold Change -MYCN 4.464 -MET 2.173 -MYC 4.76 - -[Splice Variants] -Gene Affected Exon Breakpoint 1 Breakpoint 2 Splice Supporting Reads Reference Reads Transcript -NA - -[Fusions] -Gene Pair Breakpoint 1 Breakpoint 2 Fusion Supporting Reads Gene 1 Reference Reads Gene 2 Reference Reads -NA - -[Small Variants] -Gene Chromosome Genomic Position Reference Call Alternative Call Allele Frequency Depth P-Dot Notation C-Dot Notation Consequence(s) Affected Exon(s) -TNFRSF14 chr1 2488153 A G 0.3967 910 NP_003811.2:p.(Lys17Arg) NM_003820.3:c.50A>G missense_variant 1/8 -TNFRSF14 chr1 2489805 G A 0.0936 1240 NP_003811.2:p.(Gly68Arg) NM_003820.3:c.202G>A missense_variant 3/8 -MTOR chr1 11174511 C A 0.0467 899 NM_004958.3:c.7165-1G>T splice_acceptor_variant -MTOR chr1 11288758 G A 0.7032 1388 NM_004958.3:c.2997C>T(p.(Asn999=)) NM_004958.3:c.2997C>T synonymous_variant 19/58 -MTOR chr1 11301714 A G 0.6751 1225 NM_004958.3:c.1437T>C(p.(Asp479=)) NM_004958.3:c.1437T>C synonymous_variant 10/58 -SPEN chr1 16255108 A G 0.0996 1185 NM_015001.2:c.2373A>G(p.(Thr791=)) NM_015001.2:c.2373A>G synonymous_variant 11/15 -SPEN chr1 16255644 C T 0.2316 1321 NP_055816.2:p.(Ala970Val) NM_015001.2:c.2909C>T missense_variant 11/15 - chr9 19072413 C T 0.1033 1404 -FGF14 chr13 102382362 C A 0.429 1112 NM_175929.2:c.424-3202G>T intron_variant -FGF14 chr13 102589909 C T 0.1469 1055 NM_175929.2:c.209-62263G>A intron_variant -ERCC5 chr13 103528002 G C 0.3986 1119 NP_000114.2:p.(Asp1104His) NM_000123.3:c.3310G>C missense_variant 15/15 -IRS2 chr13 110435914 G A 0.0518 791 NM_003749.2:c.2487C>T(p.(Pro829=)) NM_003749.2:c.2487C>T synonymous_variant 1/2 -IRS2 chr13 110435953 A G 0.6511 963 NM_003749.2:c.2448T>C(p.(Cys816=)) NM_003749.2:c.2448T>C synonymous_variant 1/2 -IRS2 chr13 110436232 G A 0.6667 402 NM_003749.2:c.2169C>T(p.(Ser723=)) NM_003749.2:c.2169C>T synonymous_variant 1/2 -NFKBIA chr14 35872926 G A 0.0311 1352 NM_020529.2:c.306C>T(p.(Ala102=)) NM_020529.2:c.306C>T synonymous_variant 2/6 -NFKBIA chr14 35873770 G A 0.1058 1106 NM_020529.2:c.81C>T(p.(Asp27=)) NM_020529.2:c.81C>T synonymous_variant 1/6 -NKX2-1 chr14 36986656 C A 0.1068 103 NP_001073136.1:p.(Ala345Ser) NM_001079668.2:c.1033G>T missense_variant 3/3 -NKX2-1 chr14 36991098 C G 0.0682 1525 upstream_gene_variant -FGF7 chr15 49756480 G T 0.1051 1151 NM_002009.3:c.287-18868G>T intron_variant -MAPK3 chr16 30134375 C T 0.0325 738 NM_002746.2:c.156G>A(p.(Ala52=)) NM_002746.2:c.156G>A synonymous_variant 1/9 -PRSS8 chr16 31144657 G A 0.0993 1359 NM_002773.3:c.156C>T(p.(Val52=)) NM_002773.3:c.156C>T synonymous_variant 3/6 -CYLD chr16 50827518 C T 0.1381 1072 NM_015247.2:c.2412C>T(p.(Asp804=)) NM_015247.2:c.2412C>T synonymous_variant 18/20 -AKT2 chr19 40736295 G T 0.0366 1258 NM_001626.5:c.*3484C>A 3_prime_UTR_variant 14/14 -AKT2 chr19 40737242 T C 1 1390 NM_001626.5:c.*2537= 3_prime_UTR_variant 14/14 -ARFRP1 chr20 62331839 C T 0.0409 1198 NP_003215.1:p.(Val188Met) NM_003224.5:c.562G>A missense_variant 8/8 -ARFRP1 chr20 62331989 T G 0.2329 1065 NM_003224.5:c.483A>C(p.(Arg161=)) NM_003224.5:c.483A>C synonymous_variant 7/8 -ARFRP1 chr20 62333536 T C 0.0739 1353 NP_003215.1:p.(Ile100Val) NM_003224.5:c.298A>G missense_variant 5/8 -EP300 chr22 41566447 G T 0.0645 1024 NP_001420.2:p.(Glu1442Ter) NM_001429.3:c.4324G>T stop_gained 27/31 -EP300 chr22 41566524 CA C 0.1877 554 NP_001420.2:p.(Met1470CysfsTer26) NM_001429.3:c.4408del frameshift_variant 27/31 -EP300 chr22 41568524 G A 0.046 630 NP_001420.2:p.(Glu1492Lys) NM_001429.3:c.4474G>A missense_variant 28/31 -EP300 chr22 41568531 G A 0.0433 693 NP_001420.2:p.(Arg1494Lys) NM_001429.3:c.4481G>A missense_variant 28/31 -KDM6A chrX 44929077 C A 0.1299 1032 NP_001278344.1:p.(Thr778Lys) NM_001291415.1:c.2333C>A missense_variant 18/30 -KDM6A chrX 44938563 G A 0.4155 722 NM_001291415.1:c.3267G>A(p.(Gln1089=)) NM_001291415.1:c.3267G>A synonymous_variant 21/30 -RBM10 chrX 47041246 G A 0.0541 1073 NM_001204468.1:c.1869G>A(p.(Gln623=)) NM_001204468.1:c.1869G>A synonymous_variant 15/24 -RBM10 chrX 47045888 C T 0.0687 728 NP_001191397.1:p.(Arg960Trp) NM_001204468.1:c.2878C>T missense_variant 24/24 - - diff --git a/tests/test_data_tsv2db/sample_CombinedVariantOutput_novar.tsv b/tests/test_data_tsv2db/sample_CombinedVariantOutput_novar.tsv deleted file mode 100755 index 338b611..0000000 --- a/tests/test_data_tsv2db/sample_CombinedVariantOutput_novar.tsv +++ /dev/null @@ -1,42 +0,0 @@ -TruSight Oncology 500 - Combined Variant Output -For Research Use Only. Not for use in diagnostic procedures. - -[Analysis Details] -Pair ID 12345 -DNA Sample ID 12345 -RNA Sample ID NA -Output Date 2099-99-99 -Output Time 18:33:23 -Module Version NA -Pipeline Version 1 - -[Sequencing Run Details] -NA - -[TMB] -Total TMB 275.6 -Coding Region Size in Megabases 1.28 -Number of Passing Eligible Variants 352 - -[MSI] -Usable MSI Sites 125 -Total MSI Sites Unstable 81 -Percent Unstable MSI Sites 64.8 - -[Gene Amplifications] -Gene Fold Change -MYCN 4.464 -MET 2.173 -MYC 4.76 - -[Splice Variants] -Gene Affected Exon Breakpoint 1 Breakpoint 2 Splice Supporting Reads Reference Reads Transcript -NA - -[Fusions] -Gene Pair Breakpoint 1 Breakpoint 2 Fusion Supporting Reads Gene 1 Reference Reads Gene 2 Reference Reads -NA - -[Small Variants] -Gene Chromosome Genomic Position Reference Call Alternative Call Allele Frequency Depth P-Dot Notation C-Dot Notation Consequence(s) Affected Exon(s) -NA diff --git a/tests/test_tsv2db.py b/tests/test_tsv2db.py deleted file mode 100755 index adc8c73..0000000 --- a/tests/test_tsv2db.py +++ /dev/null @@ -1,103 +0,0 @@ -import unittest - -from tsv2db import parse_ntc_tsv, parse_sample_tsv - - -""" - -test usage: - -type 'python -m unittest' from within a directory which contains the test_tsv2db.py script and test_data folder. - -""" - -class test_tsv2db(unittest.TestCase): - - # define filepaths - test_data_location = 'test_data_tsv2db' - test_ntc_no_var = f'{test_data_location}/NTC_no_var.tsv' - test_ntc_fake = f'{test_data_location}/NTC_fake_variants.tsv' - test_ntc_no_var_blanks = f'{test_data_location}/NTC_novar_blanks.tsv' - test_sample = f'{test_data_location}/sample_CombinedVariantOutput.tsv' - test_sample_no_var = f'{test_data_location}/sample_CombinedVariantOutput_novar.tsv' - test_sample_blanks = f'{test_data_location}/sample_CombinedVariantOutput_blanks.tsv' - - - def test_parse_ntc_tsv_novar(self): - """ - test read of ntc tsv with no variants - - """ - ntc_var_list = parse_ntc_tsv(self.test_ntc_no_var) - self.assertEqual(ntc_var_list, []) - - - def test_parse_ntc_tsv_var(self): - """ - test read of first 7 columns of variant info correct - - """ - ntc_var_list = parse_ntc_tsv(self.test_ntc_fake) - self.assertEqual(ntc_var_list[0], ['TNFRSF14', 'chr1', '2489805', 'G', 'A', '0.0936', '87']) - - ## test read of first 7 columns of cariant info is correct if gene name is missing - self.assertEqual(ntc_var_list[3][0], '') - - - def test_parse_ntc_tsv_novar_blanks(self): - """ - test "NA" still output if there are extra blanks left after the first line - - """ - ntc_var_list = parse_ntc_tsv(self.test_ntc_no_var_blanks) - self.assertEqual(ntc_var_list, []) - - - def test_parse_sample_tsv_no_var(self): - """ - test that when no variants in the sample then output is empty list - - """ - ntc_var_list = parse_ntc_tsv(self.test_ntc_no_var) - sample_var_list = parse_sample_tsv(self.test_sample_no_var, ntc_var_list) - self.assertEqual(sample_var_list, []) - - - def test_parse_sample_tsv_no_ntc_var(self): - """ - test that when no variants in the NTC then all "in_ntc" column is "False" - - """ - ntc_var_list = parse_ntc_tsv(self.test_ntc_no_var) - sample_var_list = parse_sample_tsv(self.test_sample, ntc_var_list) - for item in sample_var_list: - with self.subTest(item = item): - self.assertEqual(item.split('\t')[12], 'False') - - - def test_parse_sample_tsv_var_ntc_fake(self): - """ - test that if ntc has a variant then "in_ntc" column is changed to True and 'ntc_vaf', 'ntc_depth', 'ntc_alt_reads' are populated - - """ - ntc_var_list = parse_ntc_tsv(self.test_ntc_fake) - sample_var_list = parse_sample_tsv(self.test_sample,ntc_var_list) - test_list = sample_var_list[1].split('\t') - self.assertEqual(test_list[12], 'True') - self.assertNotEqual(test_list[13], '') - self.assertNotEqual(test_list[14], '') - self.assertNotEqual(test_list[15], '') - - - def test_parse_sample_tsv_extra_blanks(self): - """ - test that extra lines at end of sample tsv file doesnt error script and doesnt put out blanks in the sample var list - - """ - ntc_var_list = parse_ntc_tsv(self.test_ntc_no_var) - sample_var_list = parse_sample_tsv(self.test_sample_blanks,ntc_var_list) - self.assertNotEqual(sample_var_list[-1], '') - - -if __name__ == '__main__': - unittest.main() diff --git a/vendorCaptureBed_100pad_updated.bed b/vendorCaptureBed_100pad_updated.bed deleted file mode 100644 index 0bece47..0000000 --- a/vendorCaptureBed_100pad_updated.bed +++ /dev/null @@ -1,1230 +0,0 @@ -chr1 836563 837135 rs_id:rs28705752 -chr1 1338738 1339307 rs_id:rs17363048 -chr1 1891716 1892294 rs_id:rs2803292 -chr1 2402256 2402831 rs_id:rs2494627 -chr1 2942934 2943513 rs_id:rs7412983 -chr1 3443699 3444275 rs_id:rs34724272 -chr1 4010415 4010990 rs_id:rs4654482 -chr1 4519065 4519639 rs_id:rs605629 -chr1 5029195 5029773 rs_id:rs12025571 -chr1 5544330 5544903 rs_id:rs9787315 -chr1 6050290 6050869 rs_id:rs806107 -chr1 6593495 6594074 rs_id:rs10864612 -chr1 7112060 7112630 rs_id:rs6577410 -chr1 7666790 7667366 rs_id:rs11590447 -chr1 8194977 8195551 rs_id:rs7529511 -chr1 8732796 8733368 rs_id:rs11121215 -chr1 9261141 9261714 rs_id:rs6693180 -chr1 9799160 9799732 rs_id:rs11588785 -chr1 10326640 10327210 rs_id:rs9332414 -chr1 10850122 10850691 rs_id:rs11121624 -chr1 11386870 11387439 rs_id:rs2982375 -chr1 11913510 11914088 rs_id:rs198375 -chr1 12508694 12509271 rs_id:rs475983 -chr1 13186967 13187540 rs_id:rs35013890 -chr1 13789442 13790019 rs_id:rs2999885 -chr1 14318449 14319031 rs_id:rs4662067 -chr1 14838403 14838978 rs_id:rs10927453 -chr1 15399734 15400302 rs_id:rs4661317 -chr1 15900209 15900785 rs_id:rs6429753 -chr1 16417749 16418320 rs_id:rs28395220 -chr1 16959479 16960059 rs_id:rs1759187 -chr1 17486393 17486970 rs_id:rs4620585 -chr1 18015213 18015790 rs_id:rs34490715 -chr1 18523082 18523658 rs_id:rs4920453 -chr1 19028072 19028643 rs_id:rs2789322 -chr1 19579727 19580299 rs_id:rs10917277 -chr1 20100046 20100618 rs_id:rs2281243 -chr1 20613261 20613835 rs_id:rs6426629 -chr1 21140771 21141348 rs_id:rs10753506 -chr1 21674041 21674619 rs_id:rs213007 -chr1 22184216 22184791 rs_id:rs4654991 -chr1 22703948 22704520 rs_id:rs11799474 -chr1 23211833 23212408 rs_id:rs309477 -chr1 23731487 23732063 rs_id:rs3889814 -chr1 24286564 24287131 rs_id:rs9424346 -chr1 24803682 24804256 rs_id:rs195734 -chr1 25327681 25328252 rs_id:rs6665019 -chr1 25842701 25843277 rs_id:rs34758180 -chr1 26373421 26373996 rs_id:rs12045468 -chr1 26950141 26950704 rs_id:rs76908673 -chr1 27022616 27024308 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=1 -chr1 27055866 27056634 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=2 -chr1 27057376 27058364 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=3 -chr1 27058896 27059559 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=4 -chr1 27087076 27087867 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=5 -chr1 27087596 27088229 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=6 -chr1 27088366 27089088 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=7 -chr1 27089191 27090040 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=8 -chr1 27092441 27093136 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=9 -chr1 27092681 27093335 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=10 -chr1 27094011 27094756 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=11 -chr1 27097331 27098095 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=12 -chr1 27098711 27099402 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=13 -chr1 27099026 27099753 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=14 -chr1 27099556 27100256 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=15 -chr1 27099761 27100666 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=16;gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=17 -chr1 27100546 27101991 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=18 -chr1 27101791 27102465 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=19 -chr1 27105186 27105936 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=20 -chr1 27105466 27107535 gene_name=ARID1A;ensemble_gene_id=ENSG00000117713;ensembl_transcript_id=ENST00000324856;exon_num=20 -chr1 27467686 27468265 rs_id:rs4631721 -chr1 28125666 28126239 rs_id:rs59170025 -chr1 28668226 28668802 rs_id:rs11247776 -chr1 29188471 29189044 rs_id:rs204077 -chr1 29696971 29697544 rs_id:rs1325279 -chr1 30198042 30198620 rs_id:rs2889447 -chr1 30708717 30709291 rs_id:rs2179163 -chr1 31231347 31231923 rs_id:rs3762297 -chr1 31759792 31760367 rs_id:rs3766289 -chr1 32292826 32293404 rs_id:rs12749138 -chr1 32975657 32976234 rs_id:rs2453244 -chr1 33524497 33525073 rs_id:rs59902060 -chr1 34047661 34048237 rs_id:rs372859 -chr1 34564607 34565184 rs_id:rs6665353 -chr1 35082902 35083476 rs_id:rs11589940 -chr1 35616947 35617522 rs_id:rs7413534 -chr1 36140687 36141269 rs_id:rs665046 -chr1 36735842 36736413 rs_id:rs67582816 -chr1 37268692 37269264 rs_id:rs488680 -chr1 37806262 37806845 rs_id:rs1022554 -chr1 38318595 38319170 rs_id:rs12743834 -chr1 38861540 38862116 rs_id:rs4970588 -chr1 39369324 39369897 rs_id:rs9438986 -chr1 39914709 39915281 rs_id:rs1180379 -chr1 40479184 40479760 rs_id:rs12410793 -chr1 41020829 41021397 rs_id:rs11811487 -chr1 41554664 41555246 rs_id:rs61781795 -chr1 42068248 42068822 rs_id:rs10890143 -chr1 42592783 42593363 rs_id:rs883239 -chr1 43099983 43100561 rs_id:rs10789420 -chr1 43623313 43623888 rs_id:rs672429 -chr1 43814928 43815035 MPL(NM_005373.2):exon_10 -chr1 44173838 44174412 rs_id:rs7528454 -chr1 44694979 44695554 rs_id:rs1738051 -chr1 45236784 45237357 rs_id:rs12136048 -chr1 45788229 45788799 rs_id:rs12026893 -chr1 46305019 46305589 rs_id:rs10890354 -chr1 46833969 46834541 rs_id:rs12075550 -chr1 47384980 47385551 rs_id:rs10890426 -chr1 47906545 47907118 rs_id:rs59349700 -chr1 48450180 48450757 rs_id:rs4927298 -chr1 48954145 48954714 rs_id:rs2253233 -chr1 49499270 49499842 rs_id:rs10888643 -chr1 50024600 50025172 rs_id:rs1305489 -chr1 50535780 50536354 rs_id:rs12127726 -chr1 51066700 51067276 rs_id:rs12083078 -chr1 51568875 51569450 rs_id:rs2026812 -chr1 52094390 52094962 rs_id:rs12041481 -chr1 52627955 52628530 rs_id:rs10888748 -chr1 53171870 53172448 rs_id:rs581114 -chr1 53713300 53713870 rs_id:rs11206127 -chr1 54215566 54216143 rs_id:rs6588488 -chr1 54753081 54753653 rs_id:rs6690777 -chr1 55259426 55259997 rs_id:rs1147988 -chr1 55803076 55803654 rs_id:rs207160 -chr1 56311596 56312171 rs_id:rs12059833 -chr1 56820315 56820897 rs_id:rs10493208 -chr1 57333426 57334004 rs_id:rs601662 -chr1 57858530 57859105 rs_id:rs4912247 -chr1 58362060 58362634 rs_id:rs1202836 -chr1 58866190 58866764 rs_id:rs338918 -chr1 59386379 59386959 rs_id:rs2716113 -chr1 59895204 59895782 rs_id:rs6587854 -chr1 60406384 60406954 rs_id:rs10889163 -chr1 60929554 60930131 rs_id:rs10889176 -chr1 61441082 61441654 rs_id:rs12562350 -chr1 61963042 61963615 rs_id:rs34458388 -chr1 62473376 62473951 rs_id:rs35402181 -chr1 62973815 62974390 rs_id:rs1168042 -chr1 63491510 63492081 rs_id:rs2225323 -chr1 64005830 64006400 rs_id:rs217450 -chr1 64508401 64508975 rs_id:rs705533 -chr1 65016347 65016922 rs_id:rs12408795 -chr1 65538917 65539497 rs_id:rs875868 -chr1 66049242 66049823 rs_id:rs4655528 -chr1 66569187 66569764 rs_id:rs2503162 -chr1 67078377 67078947 rs_id:rs4655501 -chr1 67582462 67583039 rs_id:rs6703469 -chr1 68090722 68091303 rs_id:rs787484 -chr1 68610657 68611231 rs_id:rs2052960 -chr1 69139602 69140175 rs_id:rs11209338 -chr1 69646127 69646699 rs_id:rs1360931 -chr1 70148034 70148610 rs_id:rs12729671 -chr1 70679559 70680131 rs_id:rs17131241 -chr1 71186179 71186755 rs_id:rs1115023 -chr1 71712424 71712999 rs_id:rs1431504 -chr1 72226781 72227353 rs_id:rs6692267 -chr1 72750811 72751380 rs_id:rs3101337 -chr1 73258946 73259522 rs_id:rs2259784 -chr1 73782696 73783267 rs_id:rs11210207 -chr1 74331281 74331853 rs_id:rs4649994 -chr1 74856112 74856689 rs_id:rs6424589 -chr1 75369093 75369660 rs_id:rs1327093 -chr1 75918419 75918990 rs_id:rs60222754 -chr1 76450854 76451434 rs_id:rs1251560 -chr1 76960804 76961379 rs_id:rs12742787 -chr1 77472834 77473406 rs_id:rs12065122 -chr1 77992452 77993025 rs_id:rs2803136 -chr1 78494481 78495055 rs_id:rs7524504 -chr1 79033464 79034036 rs_id:rs603546 -chr1 79549364 79549939 rs_id:rs1571993 -chr1 80098979 80099551 rs_id:rs11162765 -chr1 80607840 80608419 rs_id:rs12144259 -chr1 81113210 81113786 rs_id:rs11163072 -chr1 81620507 81621077 rs_id:rs6682877 -chr1 82121602 82122180 rs_id:rs6672464 -chr1 82627216 82627792 rs_id:rs12077681 -chr1 83129330 83129912 rs_id:rs61765361 -chr1 83955840 83956416 rs_id:rs7516943 -chr1 84471410 84471983 rs_id:rs657134 -chr1 84988765 84989339 rs_id:rs74095436 -chr1 85536635 85537210 rs_id:rs4907130 -chr1 86063695 86064273 rs_id:rs4949913 -chr1 86581900 86582477 rs_id:rs1108309 -chr1 87087735 87088306 rs_id:rs2176496 -chr1 87603995 87604577 rs_id:rs4415539 -chr1 88122650 88123218 rs_id:rs28450337 -chr1 88625387 88625963 rs_id:rs12032672 -chr1 89143518 89144089 rs_id:rs923600 -chr1 89662088 89662662 rs_id:rs605339 -chr1 90174519 90175092 rs_id:rs1320562 -chr1 90686193 90686768 rs_id:rs12410130 -chr1 91192802 91193371 rs_id:rs10922907 -chr1 91735667 91736248 rs_id:rs1583818 -chr1 92274087 92274665 rs_id:rs284153 -chr1 92808087 92808666 rs_id:rs7528377 -chr1 93412267 93412843 rs_id:rs4847385 -chr1 93984557 93985134 rs_id:rs4847431 -chr1 94516141 94516716 rs_id:rs4147836 -chr1 95050136 95050711 rs_id:rs1146473 -chr1 95553962 95554536 rs_id:rs7512953 -chr1 96087862 96088437 rs_id:rs621485 -chr1 96596722 96597303 rs_id:rs1402807 -chr1 97111522 97112098 rs_id:rs9787359 -chr1 97544252 97544967 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=23 -chr1 97547607 97548301 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=22 -chr1 97563777 97564460 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=21 -chr1 97632672 97633247 rs_id:rs993714 -chr1 97658347 97659081 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=20 -chr1 97700127 97700829 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=19 -chr1 97770537 97771206 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=18 -chr1 97771462 97772129 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=17 -chr1 97838847 97839479 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=16 -chr1 97847682 97848281 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=15 -chr1 97915297 97916056 gene=DPYD;variant=c.1905+1G>A;gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=14 -chr1 97981007 97981765 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=13 -chr1 98014847 98015580 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=12 -chr1 98039042 98039799 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=11 -chr1 98058507 98059320 gene=DPYD;variant=c.959-51T>C;gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=10 -chr1 98060347 98060994 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=9 -chr1 98144382 98145017 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=8 -chr1 98156992 98157634 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=7 -chr1 98164467 98165091 gene=DPYD;variant=c.680+139G>A -chr1 98164637 98165378 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=6 -chr1 98186722 98187504 gene=DPYD;variant=c.483+18G>A;gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=5 -chr1 98205672 98206314 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=4 -chr1 98218027 98218607 rs_id:rs56202188 -chr1 98293397 98294025 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=3 -chr1 98348552 98349205 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=2 -chr1 98386172 98386756 gene_name=DPYD;ensemble_gene_id=ENSG00000188641;ensembl_transcript_id=ENST00000370192;exon_num=1 -chr1 98764182 98764759 rs_id:rs12120750 -chr1 99319522 99320094 rs_id:rs1351560 -chr1 99837312 99837886 rs_id:rs2182327 -chr1 100367137 100367709 rs_id:rs2769698 -chr1 100906242 100906818 rs_id:rs3767830 -chr1 101459387 101459954 rs_id:rs6675353 -chr1 101972717 101973295 rs_id:rs374982 -chr1 102507767 102508337 rs_id:rs4133019 -chr1 103021987 103022568 rs_id:rs1517422 -chr1 103557832 103558411 rs_id:rs12142575 -chr1 104109713 104110292 rs_id:rs10159229 -chr1 104618248 104618823 rs_id:rs6671116 -chr1 105154908 105155485 rs_id:rs4396129 -chr1 105670010 105670588 rs_id:rs7554044 -chr1 106172384 106172960 rs_id:rs2689981 -chr1 106677061 106677639 rs_id:rs4465236 -chr1 107223391 107223971 rs_id:rs12045424 -chr1 107775131 107775706 rs_id:rs5012609 -chr1 108283936 108284508 rs_id:rs6583043 -chr1 108870911 108871485 rs_id:rs1417300 -chr1 109415903 109416471 rs_id:rs12090453 -chr1 110052816 110053385 rs_id:rs919958 -chr1 110598331 110598906 rs_id:rs10745308 -chr1 111113617 111114195 rs_id:rs923827 -chr1 111645342 111645915 rs_id:rs1282261 -chr1 112148037 112148609 rs_id:rs2786989 -chr1 112658274 112658857 rs_id:rs1440161 -chr1 113179353 113179926 rs_id:rs6537747 -chr1 113712133 113712708 rs_id:rs4838978 -chr1 114220413 114220982 rs_id:rs10776773 -chr1 114738298 114738868 rs_id:rs596213 -chr1 115251918 115252627 gene_name=NRAS;ensemble_gene_id=ENSG00000213281;ensembl_transcript_id=ENST00000369535;exon_num=4 -chr1 115256148 115256867 gene_name=NRAS;ensemble_gene_id=ENSG00000213281;ensembl_transcript_id=ENST00000369535;exon_num=3 -chr1 115256521 115256536 NRAS(NM_002524.4):codon_61 -chr1 115258403 115259057 gene_name=NRAS;ensemble_gene_id=ENSG00000213281;ensembl_transcript_id=ENST00000369535;exon_num=2 -chr1 115258736 115258754 NRAS(NM_002524.4):codons_12-13 -chr1 115297127 115297705 rs_id:rs10858053 -chr1 115818451 115819026 rs_id:rs2982742 -chr1 116337942 116338519 rs_id:rs7520087 -chr1 116899538 116900117 rs_id:rs6680109 -chr1 117431628 117432196 rs_id:rs7366080 -chr1 117958918 117959490 rs_id:rs11807022 -chr1 118498804 118499376 rs_id:rs4658973 -chr1 119000929 119001501 rs_id:rs1575619 -chr1 119531164 119531733 rs_id:rs1106529 -chr1 120059249 120059816 rs_id:rs10923844 -chr1 120443371 120443947 rs_id:rs2793826 -chr1 121161701 121162264 rs_id:rs6693211 -chr1 154140128 154140704 gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=10 -chr1 154141498 154142152 gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=9 -chr1 154142588 154143232 gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=8 -chr1 154142838 154143481 gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=7 -chr1 154143613 154144235 gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=6 -chr1 154145093 154145860 gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=4;gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=5 -chr1 154145378 154146007 gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=4 -chr1 154148273 154148896 gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=3 -chr1 154148438 154149052 gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=3 -chr1 154163395 154164055 gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=2 -chr1 154164075 154164798 gene_name=TPM3;ensemble_gene_id=ENSG00000143549;ensembl_transcript_id=ENST00000368530;exon_num=1 -chr1 156830449 156831213 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=1 -chr1 156833869 156834497 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=2 -chr1 156834244 156834870 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=3 -chr1 156836434 156837048 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=4 -chr1 156837619 156838320 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=5 -chr1 156838019 156838712 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=6 -chr1 156841144 156841827 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=7 -chr1 156843144 156844028 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=8 -chr1 156843894 156844469 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=9 -chr1 156844094 156844697 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=10 -chr1 156844424 156845080 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=11 -chr1 156845034 156845736 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=12 -chr1 156845594 156846276 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=13 -chr1 156845914 156846643 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=14 -chr1 156848634 156849432 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=15 -chr1 156849514 156850228 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=16 -chr1 156850974 156851697 gene_name=NTRK1;ensemble_gene_id=ENSG00000198400;ensembl_transcript_id=ENST00000524377;exon_num=17 -chr1 226251731 226252372 gene_name=H3F3A;ensemble_gene_id=ENSG00000163041;ensembl_transcript_id=ENST00000366815;exon_num=2 -chr1 226251901 226252505 gene_name=H3F3A;ensemble_gene_id=ENSG00000163041;ensembl_transcript_id=ENST00000366815;exon_num=2 -chr2 25457142 25457294 DNMT3A(NM_175629.2):exon_23 -chr2 25458570 25458699 DNMT3A(NM_175629.2):exon_22 -chr2 25459799 25459879 DNMT3A(NM_175629.2):exon_21 -chr2 25461993 25462089 DNMT3A(NM_175629.2):exon_20 -chr2 25463165 25463324 DNMT3A(NM_175629.2):exon_19 -chr2 25463503 25463604 DNMT3A(NM_175629.2):exon_18 -chr2 25464425 25464581 DNMT3A(NM_175629.2):exon_17 -chr2 25466761 25466856 DNMT3A(NM_175629.2):exon_16 -chr2 25467018 25467212 DNMT3A(NM_175629.2):exon_15 -chr2 25467403 25467526 DNMT3A(NM_175629.2):exon_14 -chr2 25468116 25468206 DNMT3A(NM_175629.2):exon_13 -chr2 25468883 25468938 DNMT3A(NM_175629.2):exon_12 -chr2 25469023 25469183 DNMT3A(NM_175629.2):exon_11 -chr2 25469483 25469650 DNMT3A(NM_175629.2):exon_10 -chr2 25469914 25470032 DNMT3A(NM_175629.2):exon_9 -chr2 25470454 25470623 DNMT3A(NM_175629.2):exon_8 -chr2 25470900 25471126 DNMT3A(NM_175629.2):exon_7 -chr2 25472520 25472598 DNMT3A(NM_153759.3):exon_2 -chr2 25475057 25475071 DNMT3A(NM_153759.3):exon_1 -chr2 25497804 25497961 DNMT3A(NM_175629.2):exon_6 -chr2 25498363 25498417 DNMT3A(NM_175629.2):exon_5 -chr2 25505304 25505585 DNMT3A(NM_175629.2):exon_4 -chr2 25523002 25523117 DNMT3A(NM_175629.2):exon_3 -chr2 25536776 25536858 DNMT3A(NM_175629.2):exon_2 -chr2 29445928 29446672 gene_name=ALK;ensemble_gene_id=ENSG00000171094;ensembl_transcript_id=ENST00000389048;exon_num=20 -chr2 29448058 29448710 gene_name=ALK;ensemble_gene_id=ENSG00000171094;ensembl_transcript_id=ENST00000389048;exon_num=19 -chr2 42396484 42397056 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=1 -chr2 42472389 42473106 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=2 -chr2 42483374 42484043 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=3 -chr2 42487959 42488737 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=4 -chr2 42490049 42490718 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=5 -chr2 42491569 42492151 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=6 -chr2 42507719 42508379 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=7 -chr2 42509694 42510388 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=8 -chr2 42511504 42512123 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=9 -chr2 42513139 42513791 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=10 -chr2 42515099 42515740 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=11 -chr2 42521989 42522672 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=12 -chr2 42522244 42522933 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=13 -chr2 42528114 42528807 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=14 -chr2 42529969 42530645 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=15 -chr2 42530184 42530865 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=16 -chr2 42531349 42531966 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=17 -chr2 42542834 42543459 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=18 -chr2 42544289 42544936 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=19 -chr2 42552339 42552971 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=20 -chr2 42553024 42553661 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=21 -chr2 42555759 42556426 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=22 -chr2 42556604 42557625 gene_name=EML4;ensemble_gene_id=ENSG00000143924;ensembl_transcript_id=ENST00000318522;exon_num=23 -chr2 198266460 198266617 SF3B1(NM_012433.3):exon_16 -chr2 198266703 198266859 SF3B1(NM_012433.3):exon_15 -chr2 198267274 198267555 SF3B1(NM_012433.3):exon_14 -chr2 198267667 198267764 SF3B1(NM_012433.3):exon_13 -chr2 209112790 209113658 gene=IDH1;gene=IDH1;variant=IDH1_p.132 -chr2 209113104 209113119 IDH1(NM_005896.3):codon_R132 -chr3 49412861 49413027 RHOA(NM001664.3):exon_2 -chr3 128199856 128200166 GATA2(NM_032638.4):exon_7 -chr3 128200656 128200792 GATA2(NM_032638.4):exon_6 -chr3 128202697 128202853 GATA2(NM_032638.4):exon_5 -chr3 128204564 128205216 GATA2(NM_032638.4):exon_4 -chr3 128205640 128205879 GATA2(NM_032638.4):exon_3 -chr3 178771922 178772498 rs_id:rs4256180 -chr3 178780664 178781242 gene_name=PIK3CA -chr3 178791427 178792005 rs_id:rs9861291 -chr3 178800759 178801337 gene_name=PIK3CA -chr3 178810659 178811232 gene_name=PIK3CA -chr3 178817562 178818138 rs_id:rs885350 -chr3 178827127 178827702 rs_id:rs7372645 -chr3 178840902 178841473 rs_id:rs4854965 -chr3 178853742 178854318 rs_id:rs7611081 -chr3 178860774 178861342 gene_name=PIK3CA -chr3 178871577 178872141 rs_id:rs11919383 -chr3 178880844 178881416 gene_name=PIK3CA -chr3 178890407 178890979 rs_id:rs7644648 -chr3 178901069 178901647 gene_name=PIK3CA -chr3 178907602 178908173 rs_id:rs9866361 -chr3 178916334 178917245 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=2 -chr3 178917209 178917963 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=3 -chr3 178918799 178919600 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=4 -chr3 178921064 178921855 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=5 -chr3 178922024 178922637 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=6 -chr3 178924697 178925269 rs_id:rs6803219 -chr3 178927114 178927762 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=7 -chr3 178927704 178928405 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=8 -chr3 178927949 178928629 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=9 -chr3 178935729 178936394 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=10 -chr3 178936714 178937327 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=11 -chr3 178937089 178937789 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=12 -chr3 178937469 178938112 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=13 -chr3 178938504 178939223 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=14 -chr3 178940247 178940820 rs_id:rs67920954 -chr3 178941599 178942251 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=15 -chr3 178942219 178942870 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=16 -chr3 178943469 178944106 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=17 -chr3 178946789 178947498 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=18 -chr3 178947514 178948175 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=19 -chr3 178947734 178948440 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=20 -chr3 178951604 178952432 gene_name=PIK3CA;ensemble_gene_id=ENSG00000121879;ensembl_transcript_id=ENST00000263967;exon_num=21 -chr3 178962827 178963405 rs_id:rs9829903 -chr3 178973387 178973964 rs_id:rs10936995 -chr3 178981069 178981646 gene_name=PIK3CA -chr3 178986752 178987328 rs_id:rs7641524 -chr3 178994469 178995046 gene_name=PIK3CA -chr3 179005452 179006031 rs_id:rs11714155 -chr3 179015912 179016484 rs_id:rs9879306 -chr3 179021094 179021678 gene_name=PIK3CA -chr3 179032392 179032965 rs_id:rs13076106 -chr3 179040894 179041464 gene_name=PIK3CA -chr3 179050874 179051459 gene_name=PIK3CA -chr4 1803245 1803248 FGFR3(NM_000142.4):codon_R200 -chr4 1803563 1803566 FGFR3(NM_000142.4):codon_R248 -chr4 1803566 1803569 FGFR3(NM_000142.4):codon_S249 -chr4 1805511 1805514 FGFR3(NM_000142.4):codon_G342 -chr4 1806056 1806247 FGFR3(NM_000142.4):exon_9 -chr4 1806088 1806091 FGFR3(NM_000142.4):codon_G370 -chr4 1806091 1806094 FGFR3(NM_000142.4):codon_S371 -chr4 1806097 1806100 FGFR3(NM_000142.4):codon_Y373 -chr4 1806103 1806106 FGFR3(NM_000142.4):codon_G375 -chr4 1806118 1806121 FGFR3(NM_000142.4):codon_G380 -chr4 1806151 1806154 FGFR3(NM_000142.4):codon_A391 -chr4 1807332 1807335 FGFR3(NM_000142.4):codon_M528 -chr4 1807368 1807371 FGFR3(NM_000142.4):codon_N540 -chr4 1807493 1807496 FGFR3(NM_000142.4):codon_V555 -chr4 1807801 1807804 FGFR3(NM_000142.4):codon_R621 -chr4 1807861 1807864 FGFR3(NM_000142.4):codon_D641 -chr4 1807888 1807891 FGFR3(NM_000142.4):codon_K650 -chr4 25663852 25664513 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=2 -chr4 25664052 25664739 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=3 -chr4 25665557 25666226 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=4 -chr4 25667482 25668170 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=5 -chr4 25669227 25669885 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=6 -chr4 25671002 25671740 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=7 -chr4 25672082 25672733 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=8 -chr4 25672942 25673622 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=9 -chr4 25674432 25675153 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=10 -chr4 25675642 25676299 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=11 -chr4 25675857 25676527 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=12 -chr4 25677477 25678648 gene_name=SLC34A2;ensemble_gene_id=ENSG00000157765;ensembl_transcript_id=ENST00000382051;exon_num=13 -chr4 55140731 55141419 gene_name=PDGFRA;ensemble_gene_id=ENSG00000134853;ensembl_transcript_id=ENST00000257290;exon_num=12 -chr4 55141002 55141145 PDGFRA(NM_006206.5):exon_12 -chr4 55143796 55144449 gene_name=PDGFRA;ensemble_gene_id=ENSG00000134853;ensembl_transcript_id=ENST00000257290;exon_num=14 -chr4 55144057 55144178 PDGFRA(NM_006206.5):exon_14 -chr4 55151736 55152408 gene_name=PDGFRA;ensemble_gene_id=ENSG00000134853;ensembl_transcript_id=ENST00000257290;exon_num=18 -chr4 55152002 55152135 PDGFRA(NM_006206.5):exon_18 -chr4 55152100 55152115 PDGFRA(NM_006206.5):codon_S847 -chr4 55591756 55592487 gene_name=KIT;ensemble_gene_id=ENSG00000157404;ensembl_transcript_id=ENST00000288135;exon_num=9 -chr4 55593311 55593985 gene_name=KIT;ensemble_gene_id=ENSG00000157404;ensembl_transcript_id=ENST00000288135;exon_num=11 -chr4 55593901 55594564 gene_name=KIT;ensemble_gene_id=ENSG00000157404;ensembl_transcript_id=ENST00000288135;exon_num=13 -chr4 55595221 55595921 gene_name=KIT;ensemble_gene_id=ENSG00000157404;ensembl_transcript_id=ENST00000288135;exon_num=14 -chr4 55598966 55599634 gene_name=KIT;ensemble_gene_id=ENSG00000157404;ensembl_transcript_id=ENST00000288135;exon_num=17 -chr4 55599230 55599363 KIT(NM_000222.2):exon_17 -chr4 106155094 106158602 TET2(NM_001127208.2):exon_3 -chr4 106162490 106162591 TET2(NM_001127208.2):exon_4 -chr4 106163985 106164089 TET2(NM_001127208.2):exon_5 -chr4 106164721 106164940 TET2(NM_001127208.2):exon_6 -chr4 106180770 106180931 TET2(NM_001127208.2):exon_7 -chr4 106182910 106183010 TET2(NM_001127208.2):exon_8 -chr4 106190761 106190909 TET2(NM_001127208.2):exon_9 -chr4 106193715 106194080 TET2(NM_001127208.2):exon_10 -chr4 106196199 106197681 TET2(NM_001127208.2):exon_11 -chr5 1294912 1295578 gene_name=TERT;type=promoter_variant -chr5 149781523 149782103 gene_name=CD74;ensemble_gene_id=ENSG00000019582;ensembl_transcript_id=ENST00000353334;exon_num=8 -chr5 149781858 149782464 gene_name=CD74;ensemble_gene_id=ENSG00000019582;ensembl_transcript_id=ENST00000353334;exon_num=7 -chr5 149782413 149783149 gene=CD47 -chr5 149783973 149784594 gene_name=CD74;ensemble_gene_id=ENSG00000019582;ensembl_transcript_id=ENST00000353334;exon_num=6 -chr5 149784368 149785008 gene_name=CD74;ensemble_gene_id=ENSG00000019582;ensembl_transcript_id=ENST00000353334;exon_num=5 -chr5 149785543 149786160 gene_name=CD74;ensemble_gene_id=ENSG00000019582;ensembl_transcript_id=ENST00000353334;exon_num=4 -chr5 149786173 149786800 gene_name=CD74;ensemble_gene_id=ENSG00000019582;ensembl_transcript_id=ENST00000353334;exon_num=3 -chr5 149786438 149787165 gene_name=CD74;ensemble_gene_id=ENSG00000019582;ensembl_transcript_id=ENST00000353334;exon_num=2 -chr5 149791918 149792591 gene_name=CD74;ensemble_gene_id=ENSG00000019582;ensembl_transcript_id=ENST00000353334;exon_num=1 -chr5 170837525 170837574 NPM1(NM_002520.6):exon_11 -chr6 117609383 117610238 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=43 -chr6 117621868 117622567 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=42 -chr6 117629683 117630367 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=41 -chr6 117630973 117631713 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=40 -chr6 117631903 117632556 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=39 -chr6 117638028 117638712 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=38 -chr6 117639083 117639681 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=37 -chr6 117640758 117641462 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=36 -chr6 117642148 117642832 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=35 -chr6 117645228 117645858 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=34 -chr6 117647108 117647853 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=33 -chr6 117650223 117650870 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=32 -chr6 117658058 117658770 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=31 -chr6 117662028 117662748 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=30 -chr6 117662288 117663073 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=29 -chr6 117663288 117663975 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=28 -chr6 117664953 117665704 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=27 -chr6 117673883 117674601 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=26 -chr6 117677523 117678344 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=25 -chr6 117678698 117679452 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=24 -chr6 117680703 117681443 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=23 -chr6 117681238 117681848 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=22 -chr6 117683498 117684298 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=21 -chr6 117685948 117686634 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=20 -chr6 117686463 117687180 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=19 -chr6 117686968 117687731 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=18 -chr6 117699943 117700599 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=17 -chr6 117704213 117704933 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=16 -chr6 117706573 117707300 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=15 -chr6 117707773 117708430 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=14 -chr6 117708663 117709472 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=13 -chr6 117710233 117711279 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=12 -chr6 117714113 117714749 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=11 -chr6 117715048 117715787 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=10 -chr6 117715498 117716179 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=9 -chr6 117717083 117717704 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=8 -chr6 117717803 117718552 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=7 -chr6 117724023 117724713 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=6 -chr6 117725163 117725856 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=5 -chr6 117730468 117731085 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=4 -chr6 117737153 117737756 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=3 -chr6 117739353 117739937 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=2 -chr6 117746428 117747087 gene_name=ROS1;ensemble_gene_id=ENSG00000047936;ensembl_transcript_id=ENST00000368508;exon_num=1 -chr6 152265139 152265781 gene=ESR1;variant=ESR1_p.303 -chr6 152332524 152333205 gene_name=ESR1;ensemble_gene_id=ENSG00000091831;ensembl_transcript_id=ENST00000206249;exon_num=5 -chr6 152415174 152415888 gene=ESR1;variant=ESR1_p.463 -chr6 152419589 152420377 gene_name=ESR1;ensemble_gene_id=ENSG00000091831;ensembl_transcript_id=ENST00000206249;exon_num=8 -chr6 159187665 159188384 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=14 -chr6 159188000 159188827 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=13 -chr6 159190085 159190730 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=12 -chr6 159190540 159191255 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=11 -chr6 159191515 159192204 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=10 -chr6 159191995 159192717 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=9 -chr6 159197165 159197813 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=8 -chr6 159204285 159204975 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=7 -chr6 159205375 159206051 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=6 -chr6 159206070 159206877 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=5 -chr6 159207870 159208504 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=4 -chr6 159210050 159210670 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=3 -chr6 159238835 159239404 gene_name=EZR;ensemble_gene_id=ENSG00000092820;ensembl_transcript_id=ENST00000367075;exon_num=2 -chr7 54989076 54989654 rs_id:rs11238338 -chr7 55006666 55007240 gene_name=EGFR -chr7 55011556 55012137 gene_name=EGFR -chr7 55020406 55020976 rs_id:rs11238340 -chr7 55026756 55027334 gene_name=EGFR -chr7 55032746 55033320 rs_id:rs1990508 -chr7 55043671 55044238 rs_id:rs10899767 -chr7 55057756 55058340 rs_id:rs4947960 -chr7 55069286 55069866 rs_id:rs1158657 -chr7 55076926 55077509 gene_name=EGFR -chr7 55086691 55087335 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=1 -chr7 55089121 55089697 rs_id:rs12718937 -chr7 55096681 55097255 gene_name=EGFR -chr7 55106631 55107208 gene_name=EGFR -chr7 55116631 55117208 gene_name=EGFR -chr7 55131336 55131912 rs_id:rs12669701 -chr7 55136761 55137344 gene_name=EGFR -chr7 55146941 55147522 gene_name=EGFR -chr7 55156631 55157209 gene_name=EGFR -chr7 55162086 55162666 rs_id:rs11977660 -chr7 55172436 55173013 rs_id:rs2110290 -chr7 55182006 55182568 rs_id:rs4947976 -chr7 55191921 55192500 rs_id:rs13244925 -chr7 55207946 55208521 rs_id:rs4947982 -chr7 55209711 55210391 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=2 -chr7 55210731 55211452 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=3 -chr7 55214031 55214712 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=4 -chr7 55218706 55219320 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=5 -chr7 55219366 55219945 rs_id:rs2075112 -chr7 55219961 55220631 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=6 -chr7 55221426 55222125 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=7 -chr7 55223256 55223911 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=8 -chr7 55223946 55224631 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=9 -chr7 55224181 55224798 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=10 -chr7 55225081 55225722 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=11 -chr7 55227561 55228297 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=12 -chr7 55228911 55229600 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=13 -chr7 55231156 55231778 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=14 -chr7 55232701 55233395 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=15 -chr7 55233616 55234195 rs_id:rs9649769 -chr7 55238601 55239186 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=16 -chr7 55240401 55241084 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=17 -chr7 55241341 55242014 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=18 -chr7 55242146 55242784 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=19 -chr7 55243481 55244056 rs_id:rs11514996 -chr7 55248706 55249439 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=20 -chr7 55253701 55254280 rs_id:rs2075107 -chr7 55259141 55259847 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=21 -chr7 55260191 55260812 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=22 -chr7 55265691 55266266 rs_id:rs2472520 -chr7 55266136 55266836 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=23 -chr7 55267741 55268379 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=24 -chr7 55268601 55269316 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=25 -chr7 55269161 55269750 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=26 -chr7 55269931 55270594 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=27 -chr7 55272681 55273586 gene_name=EGFR;ensemble_gene_id=ENSG00000146648;ensembl_transcript_id=ENST00000275493;exon_num=28 -chr7 55279421 55279992 rs_id:rs940806 -chr7 55290076 55290650 rs_id:rs6975097 -chr7 55299551 55300121 rs_id:rs7807087 -chr7 55309506 55310084 rs_id:rs11765224 -chr7 55316906 55317482 gene_name=EGFR -chr7 55323501 55324077 rs_id:rs35699152 -chr7 55334481 55335057 rs_id:rs10259320 -chr7 55345031 55345608 rs_id:rs10215194 -chr7 55355206 55355782 rs_id:rs940812 -chr7 55365751 55366322 rs_id:rs4948006 -chr7 55376981 55377554 rs_id:rs1110059 -chr7 55388281 55388855 rs_id:rs2103196 -chr7 55397621 55398197 rs_id:rs7783046 -chr7 55409041 55409618 rs_id:rs115509662 -chr7 55421601 55422172 rs_id:rs2331026 -chr7 116214318 116214889 rs_id:rs12706096 -chr7 116224588 116225160 rs_id:rs6466590 -chr7 116232353 116232933 gene_name=MET -chr7 116237803 116238376 rs_id:rs10229287 -chr7 116256488 116257059 rs_id:rs6960741 -chr7 116267268 116267840 rs_id:rs34388751 -chr7 116284328 116284899 rs_id:rs10215678 -chr7 116296218 116296796 rs_id:rs10253622 -chr7 116302363 116302942 gene_name=MET -chr7 116314623 116315197 rs_id:rs11767567 -chr7 116322413 116322991 gene_name=MET -chr7 116329073 116329648 rs_id:rs58131984 -chr7 116338863 116340606 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=2 -chr7 116341508 116342075 rs_id:rs2299438 -chr7 116354193 116354770 rs_id:rs38852 -chr7 116365078 116365657 rs_id:rs38857 -chr7 116371453 116372183 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=3 -chr7 116379733 116380413 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=4 -chr7 116380638 116381358 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=5 -chr7 116395133 116395845 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=6 -chr7 116397223 116397869 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=7 -chr7 116397423 116398099 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=8 -chr7 116398243 116398946 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=9 -chr7 116399178 116399814 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=10 -chr7 116402828 116403587 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=11 -chr7 116409443 116410115 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=12 -chr7 116411223 116412126 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=13;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=14;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=15;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;intron_num=13;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;intron_num=14 -chr7 116411633 116414450 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=13;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=14;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=15;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;intron_num=13;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;intron_num=14 -chr7 116413958 116415477 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=13;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=14;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=15;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;intron_num=13;gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;intron_num=14 -chr7 116417163 116417789 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=16 -chr7 116418558 116419287 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=17 -chr7 116421773 116422430 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=18 -chr7 116423088 116423792 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=19 -chr7 116431183 116431756 rs_id:rs193686 -chr7 116435428 116436121 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=20 -chr7 116435673 116436457 gene_name=MET;ensemble_gene_id=ENSG00000105976;ensembl_transcript_id=ENST00000397752;exon_num=21 -chr7 116442628 116443203 gene_name=MET -chr7 116452558 116453129 rs_id:rs41754 -chr7 116466313 116466896 rs_id:rs41769 -chr7 116472593 116473172 gene_name=MET -chr7 116479443 116480018 rs_id:rs41776 -chr7 116489698 116490270 rs_id:rs438 -chr7 116502653 116503224 gene_name=MET -chr7 116512033 116512601 rs_id:rs12706108 -chr7 116523218 116523790 rs_id:rs2237720 -chr7 116536238 116536808 rs_id:rs12674017 -chr7 138528795 138529496 gene_name=KIAA1549;ensemble_gene_id=ENSG00000122778;ensembl_transcript_id=ENST00000440172;exon_num=18 -chr7 138536700 138537277 gene_name=KIAA1549;ensemble_gene_id=ENSG00000122778;ensembl_transcript_id=ENST00000440172;exon_num=17 -chr7 138545605 138546478 gene_name=KIAA1549;ensemble_gene_id=ENSG00000122778;ensembl_transcript_id=ENST00000440172;exon_num=16 -chr7 138552445 138553149 gene_name=KIAA1549;ensemble_gene_id=ENSG00000122778;ensembl_transcript_id=ENST00000440172;exon_num=15 -chr7 138554015 138554779 gene_name=KIAA1549;ensemble_gene_id=ENSG00000122778;ensembl_transcript_id=ENST00000440172;exon_num=14 -chr7 138555625 138556380 gene_name=KIAA1549;ensemble_gene_id=ENSG00000122778;ensembl_transcript_id=ENST00000440172;exon_num=13 -chr7 138564015 138564677 gene_name=KIAA1549;ensemble_gene_id=ENSG00000122778;ensembl_transcript_id=ENST00000440172;exon_num=12 -chr7 140452807 140453458 gene_name=BRAF;ensemble_gene_id=ENSG00000157764;ensembl_transcript_id=ENST00000288602;exon_num=15 -chr7 140481107 140481773 gene_name=BRAF;ensemble_gene_id=ENSG00000157764;ensembl_transcript_id=ENST00000288602;exon_num=11 -chr7 140482552 140483232 gene_name=BRAF;ensemble_gene_id=ENSG00000157764;ensembl_transcript_id=ENST00000288602;exon_num=10 -chr7 140487077 140487655 gene_name=BRAF;ensemble_gene_id=ENSG00000157764;ensembl_transcript_id=ENST00000288602;exon_num=9 -chr7 148504732 148504803 EZH2(NM_004456.4):exon_20 -chr7 148506157 148506252 EZH2(NM_004456.4):exon_19 -chr7 148506396 148506487 EZH2(NM_004456.4):exon_18 -chr7 148507419 148507511 EZH2(NM_004456.4):exon_17 -chr7 148508711 148508817 EZH2(NM_004456.4):exon_16 -chr7 148508719 148508734 EZH2(NM_004456.4):codon_Y647 -chr7 148511045 148511234 EZH2(NM_004456.4):exon_15 -chr7 148512000 148512136 EZH2(NM_004456.4):exon_14 -chr7 148512592 148512643 EZH2(NM_004456.4):exon_13 -chr7 148513770 148513875 EZH2(NM_004456.4):exon_12 -chr7 148514308 148514488 EZH2(NM_004456.4):exon_11 -chr7 148514963 148515214 EZH2(NM_004456.4):exon_10 -chr7 148516682 148516784 EZH2(NM_004456.4):exon_9 -chr7 148523540 148523729 EZH2(NM_004456.4):exon_8 -chr7 148524250 148524363 EZH2(NM_004456.4):exon_7 -chr7 148525826 148525977 EZH2(NM_004456.4):exon_6 -chr7 148526814 148526945 EZH2(NM_004456.4):exon_5 -chr7 148529720 148529847 EZH2(NM_004456.4):exon_4 -chr7 148543556 148543695 EZH2(NM_004456.4):exon_3 -chr7 148544268 148544395 EZH2(NM_004456.4):exon_2 -chr8 38285492 38285495 FGFR1(NM_023110.2):codon_R189 -chr8 38282206 38282209 FGFR1(NM_023110.2):codon_P252 -chr8 38277212 38277215 FGFR1(NM_023110.2):codon_Y374 -chr8 38277191 38277194 FGFR1(NM_023110.2):codon_C381 -chr8 38275840 38275843 FGFR1(NM_023110.2):codon_R445 -chr8 38274848 38274851 FGFR1(NM_023110.2):codon_N546 -chr8 38273558 38273561 FGFR1(NM_023110.2):codon_V561 -chr8 38272305 38272308 FGFR1(NM_023110.2):codon_K656 -chr9 5069919 5070057 JAK2(NM_004972.3):exon_12 -chr9 5073763 5073778 JAK2(NM_004972.3):codon_V617 -chr9 21868424 21869001 rs_id:rs12553901 -chr9 21873764 21874341 gene_name=CDKN2A -chr9 21883719 21884299 rs_id:rs3928893 -chr9 21889604 21890184 gene_name=CDKN2A -chr9 21901299 21901863 rs_id:rs56213153 -chr9 21907584 21908158 gene_name=CDKN2A -chr9 21910274 21910851 gene_name=CDKN2A -chr9 21915874 21916437 rs_id:rs7849930 -chr9 21925919 21926498 rs_id:rs6475597 -chr9 21939689 21940258 rs_id:rs2811716 -chr9 21947669 21948242 gene_name=CDKN2A -chr9 21952814 21953383 rs_id:rs10757260 -chr9 21957989 21958561 gene_name=CDKN2A -chr9 21965974 21966547 rs_id:rs3731257 -chr9 21967949 21968524 gene_name=CDKN2A;ensemble_gene_id=ENSG00000147889;ensembl_transcript_id=ENST00000304494;exon_num=3 -chr9 21970624 21971481 gene_name=CDKN2A;ensemble_gene_id=ENSG00000147889;ensembl_transcript_id=ENST00000304494;exon_num=2 -chr9 21974399 21975099 gene_name=CDKN2A;ensemble_gene_id=ENSG00000147889;ensembl_transcript_id=ENST00000304494;exon_num=1 -chr9 21978649 21979225 rs_id:rs2518720 -chr9 21990134 21990704 rs_id:rs7036656 -chr9 21993864 21994588 gene=CDKN2A -chr9 21997959 21998536 gene_name=CDKN2A -chr9 22007709 22008282 gene_name=CDKN2A -chr9 22013089 22013657 rs_id:rs10811640 -chr9 22023459 22024033 rs_id:rs10965212 -chr9 22034394 22034965 rs_id:rs2151280 -chr9 22043579 22044153 rs_id:rs1333036 -chr9 22054354 22054926 rs_id:rs7874604 -chr9 22064754 22065327 rs_id:rs10811647 -chr9 22075739 22076311 rs_id:rs1831733 -chr9 22087949 22088525 gene_name=CDKN2A -chr9 87285383 87286149 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=4 -chr9 87316793 87317423 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=5 -chr9 87316983 87317611 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=6 -chr9 87322488 87323102 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=7 -chr9 87325283 87325985 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=8 -chr9 87338218 87338901 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=9 -chr9 87338868 87339547 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=10 -chr9 87342298 87343152 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=11 -chr9 87356538 87357113 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=12 -chr9 87359613 87360265 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=13 -chr9 87366633 87367279 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=14 -chr9 87475688 87476279 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=15 -chr9 87481888 87482622 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=16 -chr9 87548808 87549486 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=17 -chr9 87563098 87563828 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=18 -chr9 87569923 87570704 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=19 -chr9 87634843 87635555 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=20 -chr9 87635888 87636613 gene_name=NTRK2;ensemble_gene_id=ENSG00000148053;ensembl_transcript_id=ENST00000376214;exon_num=21 -chr9 139390517 139392015 NOTCH1(NM_017617.4):exon_34 -chr10 32304178 32304856 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=25 -chr10 32305803 32306556 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=24 -chr10 32306703 32307364 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=23 -chr10 32306973 32307586 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=22 -chr10 32307163 32307761 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=21 -chr10 32308518 32309163 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=20 -chr10 32309673 32310338 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=19 -chr10 32309878 32310483 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=18 -chr10 32310798 32311446 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=17 -chr10 32311498 32312233 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=16 -chr10 32317078 32317770 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=15 -chr10 32319733 32320479 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=14 -chr10 32321363 32321976 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=13 -chr10 32322493 32323237 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=12 -chr10 32323288 32323932 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=11 -chr10 32323433 32324062 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=11 -chr10 32324183 32324870 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=10 -chr10 32324538 32325199 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=9 -chr10 32325913 32326586 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=8 -chr10 32326178 32326796 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=7 -chr10 32326818 32327414 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=6 -chr10 32327428 32328028 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=5 -chr10 32327978 32328620 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=4 -chr10 32329033 32329661 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=3 -chr10 32337118 32337758 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=2 -chr10 32344498 32345181 gene_name=KIF5B;ensemble_gene_id=ENSG00000170759;ensembl_transcript_id=ENST00000302418;exon_num=1 -chr10 43572402 43573093 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=1 -chr10 43595637 43596445 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=2 -chr10 43597522 43598354 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=3 -chr10 43600132 43600918 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=4 -chr10 43601547 43602297 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=5 -chr10 43604202 43604952 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=6 -chr10 43606377 43607181 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=7 -chr10 43607277 43607944 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=8 -chr10 43608022 43608684 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=9 -chr10 43608737 43609401 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=10 -chr10 43609657 43610445 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=11 -chr10 43611762 43612451 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=12 -chr10 43613552 43614207 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=13 -chr10 43614712 43615466 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=14 -chr10 43615262 43615929 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=15 -chr10 43617127 43617740 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=16 -chr10 43618842 43619524 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=17 -chr10 43620062 43620704 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=18 -chr10 43621742 43622444 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=19 -chr10 43623282 43623992 gene_name=RET;ensemble_gene_id=ENSG00000165731;ensembl_transcript_id=ENST00000355710;exon_num=20 -chr10 61552396 61553147 gene_name=CCDC6;ensemble_gene_id=ENSG00000108091;ensembl_transcript_id=ENST00000263102;exon_num=9 -chr10 61553961 61554628 gene_name=CCDC6;ensemble_gene_id=ENSG00000108091;ensembl_transcript_id=ENST00000263102;exon_num=8 -chr10 61563906 61564554 gene_name=CCDC6;ensemble_gene_id=ENSG00000108091;ensembl_transcript_id=ENST00000263102;exon_num=7 -chr10 61566401 61567101 gene_name=CCDC6;ensemble_gene_id=ENSG00000108091;ensembl_transcript_id=ENST00000263102;exon_num=6 -chr10 61572116 61572830 gene_name=CCDC6;ensemble_gene_id=ENSG00000108091;ensembl_transcript_id=ENST00000263102;exon_num=5 -chr10 61574141 61574784 gene_name=CCDC6;ensemble_gene_id=ENSG00000108091;ensembl_transcript_id=ENST00000263102;exon_num=4 -chr10 61592006 61592691 gene_name=CCDC6;ensemble_gene_id=ENSG00000108091;ensembl_transcript_id=ENST00000263102;exon_num=3 -chr10 61612031 61612723 gene_name=CCDC6;ensemble_gene_id=ENSG00000108091;ensembl_transcript_id=ENST00000263102;exon_num=2 -chr10 61665611 61666454 gene_name=CCDC6;ensemble_gene_id=ENSG00000108091;ensembl_transcript_id=ENST00000263102;exon_num=1 -chr10 89523607 89524180 rs_id:rs1923261 -chr10 89533917 89534492 rs_id:rs2038554 -chr10 89546722 89547287 rs_id:rs1993845 -chr10 89553087 89553665 gene_name=PTEN -chr10 89558227 89558799 rs_id:rs12782454 -chr10 89570007 89570582 rs_id:rs12780237 -chr10 89580582 89581155 rs_id:rs3816651 -chr10 89590262 89590833 rs_id:rs1903861 -chr10 89606112 89606684 rs_id:rs10887760 -chr10 89616822 89617400 rs_id:rs11202589 -chr10 89623947 89624584 gene_name=PTEN;ensemble_gene_id=ENSG00000171862;ensembl_transcript_id=ENST00000371953;exon_num=1 -chr10 89632812 89633384 gene_name=PTEN -chr10 89642992 89643568 gene_name=PTEN -chr10 89653512 89654128 gene_name=PTEN;ensemble_gene_id=ENSG00000171862;ensembl_transcript_id=ENST00000371953;exon_num=2 -chr10 89674962 89675542 rs_id:rs1234224 -chr10 89685002 89685581 gene_name=PTEN;ensemble_gene_id=ENSG00000171862;ensembl_transcript_id=ENST00000371953;exon_num=3 -chr10 89688992 89689559 rs_id:rs1234213 -chr10 89690507 89691140 gene_name=PTEN;ensemble_gene_id=ENSG00000171862;ensembl_transcript_id=ENST00000371953;exon_num=4 -chr10 89692497 89693282 gene_name=PTEN;ensemble_gene_id=ENSG00000171862;ensembl_transcript_id=ENST00000371953;exon_num=5 -chr10 89705102 89705674 rs_id:rs2735343 -chr10 89711587 89712308 gene_name=PTEN;ensemble_gene_id=ENSG00000171862;ensembl_transcript_id=ENST00000371953;exon_num=6 -chr10 89717342 89718056 gene_name=PTEN;ensemble_gene_id=ENSG00000171862;ensembl_transcript_id=ENST00000371953;exon_num=7 -chr10 89720397 89721168 gene_name=PTEN;ensemble_gene_id=ENSG00000171862;ensembl_transcript_id=ENST00000371953;exon_num=8 -chr10 89723012 89723588 rs_id:rs532678 -chr10 89724777 89725497 gene_name=PTEN;ensemble_gene_id=ENSG00000171862;ensembl_transcript_id=ENST00000371953;exon_num=9 -chr10 89733022 89733600 gene_name=PTEN -chr10 89743117 89743698 gene_name=PTEN -chr10 89755962 89756535 rs_id:rs10430641 -chr10 89765802 89766374 rs_id:rs10887774 -chr10 89775832 89776406 rs_id:rs2785078 -chr10 89786022 89786601 rs_id:rs11202633 -chr10 89795937 89796514 rs_id:rs11202635 -chr10 89806887 89807457 rs_id:rs2673826 -chr10 89817029 89817608 rs_id:rs2785069 -chr10 89822829 89823410 gene_name=PTEN -chr10 123310899 123310929 FGFR2(NM_000141.4):exon_5_partial_p167-176 -chr10 123310818 123310821 FGFR2(NM_000141.4):codon_R203 -chr10 123298223 123298226 FGFR2(NM_000141.4):codon_R210 -chr10 123279675 123279678 FGFR2(NM_000141.4):codon_S252 -chr10 123279672 123279675 FGFR2(NM_000141.4):codon_P253 -chr10 123279612 123279666 FGFR2(NM_000141.4):exon_7_partial_p256-273 -chr10 123279630 123279633 FGFR2(NM_000141.4):codon_S267 -chr10 123279561 123279564 FGFR2(NM_000141.4):codon_W290 -chr10 123279495 123279594 FGFR2(NM_000141.4):exon_7_partial_p280-312 -chr10 123276971 123276974 FGFR2(NM_000141.4):codon_A315 -chr10 123276908 123276911 FGFR2(NM_000141.4):codon_D336 -chr10 123276890 123276893 FGFR2(NM_000141.4):codon_C342 -chr10 123276875 123276878 FGFR2(NM_000141.4):codon_S347 -chr10 123276863 123276866 FGFR2(NM_000141.4):codon_S351 -chr10 123276854 123276857 FGFR2(NM_000141.4):codon_S354 -chr10 123274801 123274804 FGFR2(NM_000141.4):codon_S372 -chr10 123274792 123274795 FGFR2(NM_000141.4):codon_Y375 -chr10 123274771 123274774 FGFR2(NM_000141.4):codon_C382 -chr10 123274744 123274747 FGFR2(NM_000141.4):codon_M391 -chr10 123274732 123274735 FGFR2(NM_000141.4):codon_V395 -chr10 123258069 123258072 FGFR2(NM_000141.4):codon_M537 -chr10 123258039 123258042 FGFR2(NM_000141.4):codon_I547 -chr10 123258033 123258036 FGFR2(NM_000141.4):codon_N549 -chr10 123256216 123256219 FGFR2(NM_000141.4):codon_V564 -chr10 123256213 123256216 FGFR2(NM_000141.4):codon_E565 -chr10 123256201 123256204 FGFR2(NM_000141.4):codon_K569 -chr10 123256057 123256060 FGFR2(NM_000141.4):codon_L617 -chr10 123247582 123247585 FGFR2(NM_000141.4):codon_E636 -chr10 123247567 123247570 FGFR2(NM_000141.4):codon_K641 -chr10 123247513 123247516 FGFR2(NM_000141.4):codon_K659 -chr10 123246932 123246935 FGFR2(NM_000141.4):codon_R664 -chr10 123246890 123246893 FGFR2(NM_000141.4):codon_R678 -chr11 533490 534218 gene_name=HRAS;ensemble_gene_id=ENSG00000174775;ensembl_transcript_id=ENST00000451590;exon_num=3 -chr11 533935 534612 gene_name=HRAS;ensemble_gene_id=ENSG00000174775;ensembl_transcript_id=ENST00000451590;exon_num=2 -chr11 119148870 119149012 CBL(NM_005188.3):exon_8 -chr11 119149214 119149428 CBL(NM_005188.3):exon_9 -chr12 11803056 11803099 ETV6(NM_001987.4):exon_1 -chr12 11905378 11905518 ETV6(NM_001987.4):exon_2 -chr12 11992068 11992243 ETV6(NM_001987.4):exon_3 -chr12 12006355 12006500 ETV6(NM_001987.4):exon_4 -chr12 12022352 12022908 ETV6(NM_001987.4):exon_5 -chr12 12037373 12037526 ETV6(NM_001987.4):exon_6 -chr12 12038854 12038965 ETV6(NM_001987.4):exon_7 -chr12 12043869 12043985 ETV6(NM_001987.4):exon_8 -chr12 25378278 25378975 gene_name=KRAS;ensemble_gene_id=ENSG00000133703;ensembl_transcript_id=ENST00000256078;exon_num=4 -chr12 25379888 25380623 gene_name=KRAS;ensemble_gene_id=ENSG00000133703;ensembl_transcript_id=ENST00000256078;exon_num=3 -chr12 25380162 25380351 KRAS(NM_033360.3):exon_3 -chr12 25397933 25398589 gene_name=KRAS;ensemble_gene_id=ENSG00000133703;ensembl_transcript_id=ENST00000256078;exon_num=2 -chr12 25398202 25398323 KRAS(NM_033360.3):exon_2 -chr12 133249744 133249868 POLE(NM006231.3):c.1473+5_c.1360-5(exon14) -chr12 133250155 133250298 POLE(NM006231.3):c.1359+5_c.1227-5(exon13) -chr12 133251978 133252108 POLE(NM006231.3):c.1226+5_c.1107-5(exon12) -chr12 133252315 133252411 POLE(NM006231.3):c.1106+5_c.1021-5(exon11) -chr12 133252674 133252795 POLE(NM006231.3):c.1020+5_c.910-5(exon10) -chr12 133253126 133253244 POLE(NM006231.3):c.909+5_c.802-5(exon9) -chr13 28592598 28592731 FLT3(NM_004119.2):exon_20 -chr13 28608018 28608133 FLT3(NM_004119.2):exon_15 -chr13 28608213 28608356 FLT3(NM_004119.2):exon_14 -chr13 28608432 28608549 FLT3(NM_004119.2):exon_13 -chr13 32791261 32791837 rs_id:rs6561179 -chr13 32799796 32800373 gene_name=BRCA2 -chr13 32809596 32810173 gene_name=BRCA2 -chr13 32817286 32817859 rs_id:rs2806623 -chr13 32831311 32831884 rs_id:rs2806635 -chr13 32841841 32842420 rs_id:rs206084 -chr13 32849656 32850233 gene_name=BRCA2 -chr13 32858821 32859395 rs_id:rs1460818 -chr13 32873901 32874472 rs_id:rs2013080 -chr13 32883721 32884296 rs_id:rs206108 -chr13 32890321 32890940 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=2 -chr13 32892961 32893734 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=3 -chr13 32898936 32899598 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=4 -chr13 32899971 32900556 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=5 -chr13 32900111 32900693 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=6 -chr13 32900366 32901016 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=7 -chr13 32903306 32903908 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=8 -chr13 32904776 32905440 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=9 -chr13 32906141 32907791 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=10 -chr13 32910126 32915613 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=11 -chr13 32918436 32919068 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=12 -chr13 32919306 32919885 rs_id:rs9567576 -chr13 32920696 32921307 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=13 -chr13 32928731 32929695 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=14 -chr13 32930296 32931025 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=15 -chr13 32931611 32932332 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=16 -chr13 32934671 32935245 rs_id:rs11571717 -chr13 32936391 32937107 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=17 -chr13 32937036 32937941 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=18 -chr13 32944271 32944961 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=19 -chr13 32944816 32945512 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=20 -chr13 32945466 32946042 rs_id:rs9567609 -chr13 32950536 32951202 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=21 -chr13 32953161 32953950 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=22 -chr13 32953616 32954329 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=23 -chr13 32953876 32954555 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=24 -chr13 32956511 32957088 rs_id:rs206146 -chr13 32967136 32967709 rs_id:rs9526165 -chr13 32968556 32969343 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=25 -chr13 32970766 32971454 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=26 -chr13 32972031 32973175 gene_name=BRCA2;ensemble_gene_id=ENSG00000139618;ensembl_transcript_id=ENST00000544455;exon_num=27 -chr13 32979481 32980056 gene_name=BRCA2 -chr13 32989476 32990042 rs_id:rs472873 -chr13 33000336 33000909 rs_id:rs206336 -chr13 33009686 33010269 gene_name=BRCA2 -chr13 33019601 33020173 rs_id:rs1207944 -chr13 33029361 33029943 gene_name=BRCA2 -chr13 33044576 33045150 rs_id:rs548369 -chr13 33049816 33050397 gene_name=BRCA2 -chr13 33055286 33055860 rs_id:rs169600 -chr13 33073236 33073809 rs_id:rs798265 -chr15 88419886 88420628 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=19 -chr15 88423221 88423935 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=18 -chr15 88428621 88429191 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=17 -chr15 88472151 88472939 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=16 -chr15 88475961 88476698 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=15 -chr15 88483586 88484240 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=14 -chr15 88575821 88576550 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=13 -chr15 88669231 88669870 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=12 -chr15 88670121 88670724 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=11 -chr15 88671661 88672233 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=10 -chr15 88678051 88678892 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=9 -chr15 88678861 88679547 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=8 -chr15 88679431 88680116 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=7 -chr15 88680366 88681072 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=6 -chr15 88690286 88690911 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=5 -chr15 88726381 88726995 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=4 -chr15 88727181 88727804 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=3 -chr15 88798866 88799657 gene_name=NTRK3;ensemble_gene_id=ENSG00000140538;ensembl_transcript_id=ENST00000360948;exon_num=2 -chr15 90631511 90632253 gene=IDH2;gene=IDH2;variant=IDH2_p.172 -chr15 90631813 90631984 IDH2(NM_002168.3):exon_4 -chr17 7572659 7573287 gene_name=TP53;ensemble_gene_id=ENSG00000141510;ensembl_transcript_id=ENST00000269305;exon_num=11 -chr17 7572921 7573013 TP53(NM_000546.5):exon_11 -chr17 7573659 7574313 gene_name=TP53;ensemble_gene_id=ENSG00000141510;ensembl_transcript_id=ENST00000269305;exon_num=10 -chr17 7573921 7574038 TP53(NM_000546.5):exon_10 -chr17 7576274 7576921 gene=TP53 -chr17 7576531 7576589 TP53(NM_001276695.1):exon_10 -chr17 7576579 7577203 gene_name=TP53;ensemble_gene_id=ENSG00000141510;ensembl_transcript_id=ENST00000269305;exon_num=9 -chr17 7576619 7576662 TP53(NM_001276696.1):exon_10 -chr17 7576749 7577434 gene_name=TP53;ensemble_gene_id=ENSG00000141510;ensembl_transcript_id=ENST00000269305;exon_num=8 -chr17 7576847 7576931 TP53(NM_000546.5):exon_9 -chr17 7577013 7577160 TP53(NM_000546.5):exon_8 -chr17 7577229 7577886 gene_name=TP53;ensemble_gene_id=ENSG00000141510;ensembl_transcript_id=ENST00000269305;exon_num=7 -chr17 7577493 7577613 TP53(NM_000546.5):exon_7 -chr17 7577909 7578563 gene_name=TP53;ensemble_gene_id=ENSG00000141510;ensembl_transcript_id=ENST00000269305;exon_num=6 -chr17 7578104 7578833 gene_name=TP53;ensemble_gene_id=ENSG00000141510;ensembl_transcript_id=ENST00000269305;exon_num=5 -chr17 7578171 7578294 TP53(NM_000546.5):exon_6 -chr17 7578365 7578559 TP53(NM_000546.5):exon_5 -chr17 7579044 7579855 gene_name=TP53;ensemble_gene_id=ENSG00000141510;ensembl_transcript_id=ENST00000269305;exon_num=4 -chr17 7579306 7579595 TP53(NM_000546.5):exon_4 -chr17 7579429 7579999 gene_name=TP53;ensemble_gene_id=ENSG00000141510;ensembl_transcript_id=ENST00000269305;exon_num=3 -chr17 7579569 7580188 gene_name=TP53;ensemble_gene_id=ENSG00000141510;ensembl_transcript_id=ENST00000269305;exon_num=2 -chr17 7579694 7579726 TP53(NM_000546.5):exon_3 -chr17 7579833 7579917 TP53(NM_000546.5):exon_2 -chr17 37745731 37746313 rs_id:rs11654954 -chr17 37753988 37754564 gene_name=ERBB2 -chr17 37767126 37767696 rs_id:rs4795388 -chr17 37774078 37774657 gene_name=ERBB2 -chr17 37780046 37780617 rs_id:rs33953566 -chr17 37794111 37794684 rs_id:rs4794817 -chr17 37801763 37802335 gene_name=ERBB2 -chr17 37807371 37807946 rs_id:rs9972882 -chr17 37814028 37814609 gene_name=ERBB2 -chr17 37824258 37824836 gene_name=ERBB2 -chr17 37831366 37831946 rs_id:rs1565920 -chr17 37844188 37844762 gene_name=ERBB2 -chr17 37855498 37856153 gene=ERBB2 -chr17 37855963 37856841 gene=ERBB2 -chr17 37858431 37859003 rs_id:rs1565923 -chr17 37862988 37863661 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=2 -chr17 37864303 37865062 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=3 -chr17 37865298 37865979 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=4 -chr17 37865798 37866402 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=5 -chr17 37866068 37866734 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=6 -chr17 37866313 37867009 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=7 -chr17 37867903 37868568 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=8 -chr17 37868308 37868961 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=9 -chr17 37870136 37870711 rs_id:rs2934967 -chr17 37871268 37871883 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=10 -chr17 37871423 37872069 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=11 -chr17 37871713 37872465 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=12 -chr17 37872273 37872956 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=13 -chr17 37872493 37873138 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=14 -chr17 37873298 37874012 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=15 -chr17 37875763 37876364 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=16 -chr17 37879298 37879987 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=17 -chr17 37879523 37880191 gene_name=ERBB2;ensemble_gene_id=ENSG00000141736;ensembl_transcript_id=ENST00000540147;exon_num=18 -chr17 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gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=31 -chrX 76812637 76813396 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=30 -chrX 76813872 76814591 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=29 -chrX 76829447 76830090 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=28 -chrX 76845025 76845690 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=27 -chrX 76848895 76849598 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=26 -chrX 76854595 76855298 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=25 -chrX 76854920 76855564 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=24 -chrX 76855630 76856303 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=23 -chrX 76871810 76872476 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=22 -chrX 76874005 76874728 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=21 -chrX 76875595 76876280 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=20 -chrX 76888420 76889144 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=19 -chrX 76888785 76889466 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=18 -chrX 76889805 76890473 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=17 -chrX 76891135 76891816 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=16 -chrX 76907330 76908033 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=15 -chrX 76907565 76908160 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=15 -chrX 76909310 76909967 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=14 -chrX 76911780 76912416 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=13 -chrX 76918600 76919322 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=12 -chrX 76919860 76920547 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=11 -chrX 76931450 76932072 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=10 -chrX 76936745 76940363 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=9 -chrX 76940150 76940774 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=8 -chrX 76944030 76944699 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=7 -chrX 76949035 76949698 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=6 -chrX 76951790 76952462 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=5 -chrX 76952800 76953403 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=4 -chrX 76953790 76954392 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=3 -chrX 76972330 76972992 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=2 -chrX 77041190 77041763 gene_name=ATRX;ensemble_gene_id=ENSG00000085224;ensembl_transcript_id=ENST00000373344;exon_num=1 From 03ac1e648c18b46eec0d27bca4fda78042e41df7 Mon Sep 17 00:00:00 2001 From: Istaisa <32853927+Istaisa@users.noreply.github.com> Date: Mon, 13 Apr 2026 13:24:54 +0100 Subject: [PATCH 2/3] update readme --- README.md | 44 +++++++++++--------------------------------- 1 file changed, 11 insertions(+), 33 deletions(-) diff --git a/README.md b/README.md index c6dc255..d57d840 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,9 @@ # TSO500_post_processing +This pipeline +* Demultiplexes with the Illumina app +* Runs the RNA samples through the Illumina app +* Submits the DNA samples to run through the [somatic_enrichment_nextflow](https://github.com/AWGL/somatic_enrichment_nextflow) pipeline ## Documentation @@ -16,30 +20,23 @@ From this folder run the command: The raw data directory must contain the SampleSheet.csv. -## To re-run DNA samples with a new referral +## To run a DNA sample -The script rerun_coverage.sh allows the coverage json file to be produced for a DNA sample with a new referral in all scenarios (analysis/ folder present or deleted). This can be run as follows, as transfer, from any location: - -`sbatch rerun_coverage.sh ` - -The new coverage file will then be present in Gathered_Results/Database/ alongside a new samples list file for upload to the database. +To run a DNA sample through the Illumina app, please run an old release (v1.1.1) ## Duty scientist responsibilites The duty scientist is responsible for the following tasks: -* Creating the TSO500 samplesheet- see below for requirements -* Signing off the run in autoqc database - for more information refer to the AutoQC sop -* Importing the data into the data into the somatic variant database - +* Signing off the run in autoqc database and GLIMS (NOTE: the RNA must now be signed off with the DNA) +* Signing off the run in SVD ## Samplesheet requirements * The samplesheet must contain the samples in the correct order for the RNA contamination results to be valid * Every NTC must be named NTC-worksheetid - ## Unit tests -Unit tests have been created against the following scripts: `tsv2db.py`, `coverage2json.py`, `fusion_check_with_ntc.py`. +Unit tests have been created against the following scripts: `fusion_check_with_ntc.py`. To run all unit tests: - copy these scripts into the `tests/` folder (relative imports not currently working, will be fixed in future version) @@ -50,34 +47,15 @@ To run all unit tests: To run tests on a specific script, follow the steps above but run `python -m unittest ` -## Adding a new DNA panel - -To add a new panel, the following needs to be changed: - -**Samplesheet generator:** -- Add the referral reason to the samplesheet generator (see SOP in Qpulse) and make sure it matches the filename of the new bed files (case sensitive) - -**Pipeline:** -- Generate bed files for the new panel - - The `hotspot_variants/*bed` bed file and `hotspot_coverage/*combined.bed` files are required - - The `hotspot_coverage/*hotspots.bed` and `hotspot_coverage/*genescreen.bed` files are optional - - Filenames should be all lowercase -- Make sure that all regions in the new panel are covered in `vendorCaptureBed_100pad_updated.bed` (the bed file file used to generate the depth of coverage file) -- Make sure that any flanking regions are added to the `TSO_extra_padding_chr.interval_list` file - Illumina bed file only goes +/- 2bp so this file contains the extra 3bp to make it +/- 5bp - -**Somatic variant database:** -- Make a new panel object in the somatic variant database that matches the filename of the new bed files (case sensitive) -- Move the new variants bed file into the `roi/variant_calling` folder in the somatic database - ## Adding a new RNA panel To add a new panel, the following needs to be changed: **Samplesheet generator:** -- Add the referral reason to the samplesheet generator (see SOP in Qpulse) +- Add the referral to the SampleSheet Generator, including the mapped test directory code **Pipeline:** - Add a new file to RNA_referrals named .txt with the gene names on the panel, one per line **Somatic variant database:** -- Make a new panel object in the somatic variant database that includes the genes on the panel to filter fusions by +- Make a new Panel object in SVD From 5db8a7dbd1fc32e60e3b08470eab33980d2ad90e Mon Sep 17 00:00:00 2001 From: Istaisa <32853927+Istaisa@users.noreply.github.com> Date: Mon, 13 Apr 2026 13:28:02 +0100 Subject: [PATCH 3/3] remove unnecessary conda environment and activation --- 2_TSO500.sh | 5 ----- env/pysam.yml | 7 ------- 2 files changed, 12 deletions(-) delete mode 100644 env/pysam.yml diff --git a/2_TSO500.sh b/2_TSO500.sh index b0b4c06..bfdbada 100755 --- a/2_TSO500.sh +++ b/2_TSO500.sh @@ -93,11 +93,6 @@ done # Gather QC metrics for sample ############################################################################################## -# activate conda env -set +u -conda activate TSO500_post_processing -set -u - # function to check FASTQC output count_qc_fails() { #count how many core FASTQC tests failed diff --git a/env/pysam.yml b/env/pysam.yml deleted file mode 100644 index 45e30ca..0000000 --- a/env/pysam.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: pysam -channels: - - bioconda - - defaults -dependencies: - - pysam=0.15.3 - - python=3.7.13