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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 distributions at numerous points in the pipeline

enhancementNew feature or requestNew feature or request

Status: Open.

#881 In broadinstitute/gatk-sv;

· kjaisingh opened on Nov 4, 2025

Miscalibrated evidence distributions can cause problems downstream - provide reference distributions

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

large INV lost during CPX resolve

Status: Open.

#848 In broadinstitute/gatk-sv;

· xuefzhao opened on Jul 31, 2025

Handle missing parents in PED file

Status: Open.

#845 In broadinstitute/gatk-sv;

· epiercehoffman opened on Jul 29, 2025

FYI: Extended Manta runtimes treated with RRR disabled

optimization

Status: Open.

#841 In broadinstitute/gatk-sv;

· MattWellie opened on Jul 21, 2025

gCNV makes depth-based calls on ChY on a female sample

bugSomething isn't workingSomething isn't working

Status: Open.

#824 In broadinstitute/gatk-sv;

· VJalili opened on Jun 11, 2025