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CleanVcf improvements

enhancementNew feature or requestNew feature or request

Status: Open.

#913 In broadinstitute/gatk-sv;

· kjaisingh opened on Jan 31, 2026

Inquiry regarding expected Recall performance for Single-Sample benchmarks (Illumina WGS)

Status: Open.

#910 In broadinstitute/gatk-sv;

· lmtani opened on Jan 28, 2026

Should the input .bam file be the original one generated after alignment, without undergoing duplicate marking, realignment, or base quality score recalibration?

Status: Open.

#903 In broadinstitute/gatk-sv;

· Changping-Yan opened on Dec 19, 2025

gatk-sv with Arabidopsis

Status: Open.

#898 In broadinstitute/gatk-sv;

· thugib opened on Dec 11, 2025

Running svtk from source with Python >= 3.9.23 returns an error

bugSomething isn't workingSomething isn't working

Status: Open.

#883 In broadinstitute/gatk-sv;

· kjaisingh opened on Nov 4, 2025

Infrastructure & CI/CD improvements

enhancementNew feature or requestNew feature or request

Status: Open.

#882 In broadinstitute/gatk-sv;

· kjaisingh opened on Nov 4, 2025

Provide reference distributions of variant counts and het-hom ratios

enhancementNew feature or requestNew feature or request

Status: Open.

#881 In broadinstitute/gatk-sv;

· kjaisingh opened on Nov 4, 2025

Provide reference distributions of evidence metrics and random forest cutoffs

enhancementNew feature or requestNew feature or request

Status: Open.

#880 In broadinstitute/gatk-sv;

· kjaisingh opened on Nov 4, 2025

Deprecated files in GATK-SV

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#870 In broadinstitute/gatk-sv;

· kjaisingh opened on Oct 2, 2025

SV-Shell future improvements

Status: Open.

#869 In broadinstitute/gatk-sv;

· VJalili opened on Oct 2, 2025

Handle absence of male samples in compute_AFs script

bugSomething isn't workingSomething isn't working

Status: Open.

#868 In broadinstitute/gatk-sv;

· EddieLF opened on Sep 10, 2025

Error code: Job CNVGermlineCaseWorkflow.DetermineGermlineContigPloidyCaseMode:NA:2 exited with return code 123

Status: Open.

#849 In broadinstitute/gatk-sv;

· Changping-Yan opened on Aug 1, 2025