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GATK Compatibility with CRAM 3.1

Status: Open.

#9409 In broadinstitute/gatk;

· MySelvan opened on Aug 11, 2026

Preparation of BED file for --ploidy-regions

Status: Open.

#9398 In broadinstitute/gatk;

· zhxiaokang opened on Jul 16, 2026

genomics-public-data google cloud bucket permission denied

Status: Open.

#9394 In broadinstitute/gatk;

· ypradat opened on Jul 2, 2026

Glimpse Ligate output vcf index not compatible with GATK 4.6.0

Status: Open.

#9393 In broadinstitute/gatk;

· jsotobroad opened on Jul 1, 2026

ReblockGVCF: "Query asks for data past end of contig" caused by stale position across chromosome boundary (GATK 4.6.2.0)

Status: Open.

#9392 In broadinstitute/gatk;

· shaze opened on Jun 27, 2026

AnalyzeSaturationMutagenesis does not parse modern CIGAR strings

Status: Open.

#9367 In broadinstitute/gatk;

· odcambc opened on Apr 28, 2026

AnalyzeSaturationMutagenesis does not produce HGVS-compliant output

Status: Open.

#9366 In broadinstitute/gatk;

· odcambc opened on Apr 28, 2026

GenomicsDBImport completes successfully, but SelectVariants/GenotypeGVCFs hangs at “Starting traversal” when reading gendb:// workspace

Status: Open.

#9356 In broadinstitute/gatk;

· C-YONG opened on Apr 8, 2026

changed BQ permissions - update to documentation needed

Status: Open.

#9349 In broadinstitute/gatk;

· bheavner opened on Mar 23, 2026

Remove BETA tag from VETS tools

Status: Open.

#9345 In broadinstitute/gatk;

· jonn-smith opened on Mar 11, 2026

ETA on new release built with htsjdk 4.3.0 for CRAM 3.1 support

Status: Open.

#9341 In broadinstitute/gatk;

· EddieLF opened on Mar 3, 2026

Funcotator - BRCA2 mutation with ambiguous annotation

Status: Open.

#9339 In broadinstitute/gatk;

· BarrecaM opened on Feb 27, 2026