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Mutect2 --pileup-detection true not working with a normal control?

Status: Open.

#9296 In broadinstitute/gatk;

· Rmulet opened on Oct 31, 2025

HaplotypeCaller compability problem on Windows

Status: Open.

#9293 In broadinstitute/gatk;

· MarcoLotz opened on Oct 21, 2025

Request for Review of modification to gcnvkernel

Status: Open.

#9289 In broadinstitute/gatk;

· ZerryNi opened on Oct 20, 2025

Clarification about GPU support for GATK

Status: Open.

#9282 In broadinstitute/gatk;

· samfux84 opened on Oct 13, 2025

Using GATK HapCaller/CombinesGVCFs/GenotypeGVCFs as a java library. Any drawback ?

Status: Open.

#9277 In broadinstitute/gatk;

· lindenb opened on Sep 28, 2025

MergeVcfs loses NULL sample values when SAMPLEs in headers need to be reordered

Status: Open.

#9275 In broadinstitute/gatk;

· DavidStreid opened on Sep 25, 2025

Abrubt no-error stops in HaplotypeCaller

Status: Open.

#9268 In broadinstitute/gatk;

· gevro opened on Sep 21, 2025

How to use VariantRecalibrator ?

Status: Open.

#9262 In broadinstitute/gatk;

· zznx opened on Sep 8, 2025

Some tests fail: Shared object "libm.so.6" not found, required by "libgkl_utils11425681626488905546.so"

Status: Open.

#9257 In broadinstitute/gatk;

· yurivict opened on Aug 27, 2025

Clustered Events filter is still not smart enough not to filter real somatic events.

Status: Open.

#9256 In broadinstitute/gatk;

· gokalpcelik opened on Aug 26, 2025

DetermineGermlineContigPloidy - Badly formed genome unclippedLoc

Status: Open.

#9251 In broadinstitute/gatk;

· stefandiederich opened on Aug 14, 2025

Do I need to run SplitNCigarReads before ASEReadCounter in GATK 4?

Status: Open.

#9248 In broadinstitute/gatk;

· francescoballesio opened on Aug 12, 2025