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Pull requests list

Modify genotype filtering to read cutoffs from generalizable table
#864 opened Sep 2, 2025 by kjaisingh • Draft
Bug fix missing sample ID in median coverage
#863 opened Aug 29, 2025 by VJalili Loading…
Annotate retrotransposon deletions with a filter tag enhancement New feature or request
#862 opened Aug 28, 2025 by kjaisingh Loading…
@kjaisingh
Plot SV counts for all VCFs in FilterBatchSites bug Something isn't working
#860 opened Aug 26, 2025 by epiercehoffman Loading…
Remove outdated code and documentation related to evidence assessment
#859 opened Aug 22, 2025 by epiercehoffman Loading…
2
Small updates to file names/paths in Sample QC notebook
#858 opened Aug 22, 2025 by epiercehoffman Loading…
Remove/update references to MELT
#857 opened Aug 19, 2025 by epiercehoffman Loading…
Implement a bash version of the Evidence QC workflow
#855 opened Aug 14, 2025 by VJalili Loading…
Fix code path in EvidenceQc when run_ploidy is false
#854 opened Aug 14, 2025 by mwalker174 Loading…
1
Improve RD testing to recover overlapped CNVs > 100 kbp methods
#851 opened Aug 4, 2025 by kjaisingh • Draft
@kjaisingh
Enable passing a threshold to govern the window for detection of dispersed deletions enhancement New feature or request
#850 opened Aug 2, 2025 by kjaisingh Loading…
@kjaisingh
2
Update RegenotypeCNVs.wdl GetRegenotype task
#839 opened Jul 10, 2025 by knathamuni Loading…
Update representation of BNDs to be Pysam compatible dependencies Pull requests that update a dependency file
#835 opened Jul 1, 2025 by kjaisingh • Draft
@kjaisingh
DeWDLize modules under GatherBatchEvidence
#830 opened Jun 26, 2025 by VJalili • Draft
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 • Draft
3
Ignore sites with null GTs during de novo rate calculation
#810 opened May 9, 2025 by epiercehoffman Loading…
1
Localize all the needed files, no streaming
#806 opened May 1, 2025 by VJalili • Draft
1 of 4 tasks
Introduce methods for standardized callset evaluation methods
#804 opened Apr 25, 2025 by kjaisingh • Draft
@kjaisingh
Update VM spot pricing in monitoring analysis scripts
#765 opened Jan 6, 2025 by mwalker174 Loading…
1
Migrate CleanVcf into GATK optimization
#733 opened Oct 17, 2024 by kjaisingh • Draft
@kjaisingh
Add documentation for the de-novo pipeline
#675 opened May 13, 2024 by VJalili • Draft
2 tasks
12
Refactor workflow inputs/output for consistency
#668 opened Apr 25, 2024 by VJalili • Draft
2 tasks done
Scripts to create downsampled files
#662 opened Apr 2, 2024 by VJalili Loading…
4 tasks done
Remove outliers across per-contig VCFs
#654 opened Mar 11, 2024 by epiercehoffman • Draft
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