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Deprecated files in GATK-SV

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

The stitch_fragmented_CNVs.sh script failed to produce the expected results

Status: Open.

#818 In broadinstitute/gatk-sv;

· zhangting1991 opened on Jun 7, 2025

Report null GT impact on de novo rate

Status: Open.

#807 In broadinstitute/gatk-sv;

· epiercehoffman opened on May 6, 2025

choice of reference panel for single sample workflow

Status: Open.

#801 In broadinstitute/gatk-sv;

· leqi0001 opened on Apr 21, 2025

WDL Task fails with Google Batch backend due to gcloud (RunWhamgOnCram)

bugSomething isn't workingSomething isn't working

Status: Open.

#798 In broadinstitute/gatk-sv;

· lmtani opened on Apr 15, 2025