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Pull requests list

Implement the SV Annotate module in sv-shell sv-shell SV-shell script or configuration add or update.
#886 opened Nov 7, 2025 by VJalili • Draft
Implement SV Concordance tool in sv-shell sv-shell SV-shell script or configuration add or update.
#885 opened Nov 7, 2025 by VJalili Loading…
Add the JoinRawCalls workflow to sv-shell sv-shell SV-shell script or configuration add or update.
#884 opened Nov 6, 2025 by VJalili Loading…
Update sv-shell implementation of the Gather Sample Evidence workflow sv-shell SV-shell script or configuration add or update.
#878 opened Oct 31, 2025 by VJalili • Draft
2 tasks done
Enable DRAGEN SV in single sample mode enhancement New feature or request
#875 opened Oct 21, 2025 by kjaisingh Loading…
3
Eliminate stochasticity in Median Coverage calculation enhancement New feature or request
#867 opened Sep 9, 2025 by kjaisingh Loading…
1
Modify genotype filtering to ingest cutoffs from a table enhancement New feature or request
#864 opened Sep 2, 2025 by kjaisingh Loading…
4
Annotate retrotransposon deletions with a filter tag enhancement New feature or request
#862 opened Aug 28, 2025 by kjaisingh Loading…
9
Remove outdated code and documentation related to evidence assessment
#859 opened Aug 22, 2025 by epiercehoffman Loading…
2
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…
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
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