maketube introduces structural variants and short variants to a Mycobacterium tuberculosis reference genome sequence. Variants found by aligning these genomes to the reference genome can be compared to the original ones in order to study the impact of structural variants on variant calling pipeline performances. For exemples of benchmarking pipelines, and the associated article check the sister repo adrienlemeur/maketube_supplemental. Code at adrienlemeur/maketube. Only maketube genome adrienlemeur/maketube_genomes.
If you have trouble running these tools / suggestions / comments, feel free to send me a mail at : alemeur at biophylo dot com
NOTE : you cannot directly compare SNP called from maketube genome with reference SNP without vcf2metrics.py from adrienlemeur/maketube
maketube_genomes_20x10
├── my_run_arborescence.tsv # position of every file
├── SV1 # structural variant folder
│ ├── my_run_unmuted.fasta # evolved genome without snps and indels
│ ├── pop1
│ │ ├── FASTA
│ │ │ ├── SV1_pop1_H10.fa # evolved genome with snps and indels
│ │ │ └── SV1_pop1_H10.fa.gz
│ │ ├── SV1_pop1.nwk # evolved genome reference tree
│ │ └── SV1_pop1.vcf.gz # evolved genomes reference variants
│ ├── SV1_equivalence.bed # file for vcf2metrics backtrack. Position of structural variants in the evolved genome
│ └── SV1_SV.bed # Positions of the structural variants neighbouring regions in the reference genome. Slope between 50 to 300 bp around the insertion / deletion site.
Genomes built from H37Rv, 18b and AF2122-97. Each genome has 3 sets of structural variants. Each set of structural variant has 10 haplotypes. Genome composition:
- 378-723 SNP
- 57-93 indels
- 16 Inserting Sequences jumps
- 3 Deletion Regions
- 5 - 12 ancestral-like regions
- 1 duplicated region
Genomes build from H37Rv. There are 20 sets of structural variants. Heach set of structural variant has 10 haplotypes. Genome composition:
- 1487-3196 SNP
- 88-219 indels
- 16 Inserting Sequences jumps
- 3 Deletion Regions
- 1-16 ancestral-like regions
- 1 duplicated region
Check maketube paper + supplemental for additional information.