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Pull requests: broadinstitute/gatk-sv

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Pull requests list

Modify genotype filtering to ingest cutoffs from a table enhancement New feature or request
#864 opened Sep 2, 2025 by kjaisingh Loading…
@kjaisingh
Annotate retrotransposon deletions with a filter tag enhancement New feature or request
#862 opened Aug 28, 2025 by kjaisingh Loading…
@kjaisingh
Remove outdated code and documentation related to evidence assessment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…
Improve RD testing to recover overlapped CNVs > 100 kbp methods
#851 opened Aug 4, 2025 by kjaisingh • Draft
@kjaisingh
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
Workflow to apply NCR and reference artifact filters and remove zero-carrier sites
#653 opened Mar 8, 2024 by epiercehoffman • Draft
1
fix: add sd_locs_vcf_index input to SDtoBAF
#644 opened Feb 12, 2024 by simojoe Loading…
1
2
Change default behavior of GatherSampleEvidence to skip running module metrics
#633 opened Jan 31, 2024 by VJalili • Draft
4
Removed pairwise batch effect checks from WDL workflow
#617 opened Nov 9, 2023 by shadizaheri Loading…
4
Add TransferVcfAnnotations workflow
#533 opened May 11, 2023 by mwalker174 • Draft
ProTip! Updated in the last three days: updated:>2025-09-01.