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Pull requests list

Filter variants by SVLEN before standardizing them
#955 opened Aug 7, 2026 by VJalili Member • Draft
Fix GATK gcnv env in sv-shell
#954 opened Aug 6, 2026 by VJalili Member • Draft
CleanVcf - PostHoc updates
#953 opened Aug 5, 2026 by kjaisingh Collaborator • Draft
Update reference panel resources to v1.1.1
#950 opened Jul 27, 2026 by epiercehoffman Collaborator Loading…
Add Genomic Disorder CNV calling and VCF integration
#945 opened Jun 24, 2026 by mwalker174 Collaborator Loading…
26
Fix a bug in RdTest.R
#936 opened Apr 22, 2026 by VJalili Member • Draft
Add copilot instructions
#934 opened Mar 31, 2026 by mwalker174 Collaborator Loading…
Documentation updates related to ScoreGenotypes
#928 opened Mar 10, 2026 by epiercehoffman Collaborator Loading…
Add optional use of SSD in GenotypeBatch
#924 opened Feb 26, 2026 by VJalili Member Loading…
Clean up code base
#919 opened Feb 9, 2026 by mwalker174 Collaborator • Draft
Eliminate stochasticity in Median Coverage calculation enhancement New feature or request
#867 opened Sep 9, 2025 by kjaisingh Collaborator Loading…
1
Improve RD testing to recover overlapped CNVs > 100 kbp methods
#851 opened Aug 4, 2025 by kjaisingh Collaborator • Draft
Update RegenotypeCNVs.wdl GetRegenotype task
#839 opened Jul 10, 2025 by knathamuni Contributor Loading…
fix no EVIDENCE bug in stitch_fragmented_CNVs.sh (#818)
#821 opened Jun 9, 2025 by xiaoli0 Loading…
1
Update package versions in Docker images.
#816 opened May 27, 2025 by VJalili Member • Draft
3
Ignore sites with null GTs during de novo rate calculation
#810 opened May 9, 2025 by epiercehoffman Collaborator Loading…
1
Localize all the needed files, no streaming
#806 opened May 1, 2025 by VJalili Member • Draft
1 of 4 tasks
Introduce methods for standardized callset evaluation methods
#804 opened Apr 25, 2025 by kjaisingh Collaborator • Draft
Update VM spot pricing in monitoring analysis scripts
#765 opened Jan 6, 2025 by mwalker174 Collaborator Loading…
1
Add documentation for the de-novo pipeline
#675 opened May 13, 2024 by VJalili Member • Draft
2 tasks
12
Refactor workflow inputs/output for consistency
#668 opened Apr 25, 2024 by VJalili Member • Draft
2 tasks done
Scripts to create downsampled files
#662 opened Apr 2, 2024 by VJalili Member Loading…
4 tasks done
Remove outliers across per-contig VCFs
#654 opened Mar 11, 2024 by epiercehoffman Collaborator • Draft
Workflow to apply NCR and reference artifact filters and remove zero-carrier sites
#653 opened Mar 8, 2024 by epiercehoffman Collaborator • Draft
1
fix: add sd_locs_vcf_index input to SDtoBAF
#644 opened Feb 12, 2024 by simojoe Loading…
1
2
ProTip! What’s not been updated in a month: updated:<2026-07-09.