Issues

• Funcotator mis-classifies stop-retained indels as FRAME_SHIFT_* (should be SILENT / stop-retained)

  broadinstitute/gatk#9417 · Filter by author jonn-smith opened on Aug 25, 2026

• GATK Compatibility with CRAM 3.1

  broadinstitute/gatk#9409 · Filter by author MySelvan opened on Aug 11, 2026

• Preparation of BED file for --ploidy-regions

  broadinstitute/gatk#9398 · Filter by author zhxiaokang opened on Jul 16, 2026

• genomics-public-data google cloud bucket permission denied

  broadinstitute/gatk#9394 · Filter by author ypradat opened on Jul 2, 2026

• Glimpse Ligate output vcf index not compatible with GATK 4.6.0

  broadinstitute/gatk#9393 · Filter by author 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)

  broadinstitute/gatk#9392 · Filter by author shaze opened on Jun 27, 2026

• AnalyzeSaturationMutagenesis does not parse modern CIGAR strings

  broadinstitute/gatk#9367 · Filter by author odcambc opened on Apr 28, 2026

• AnalyzeSaturationMutagenesis does not produce HGVS-compliant output

  broadinstitute/gatk#9366 · Filter by author odcambc opened on Apr 28, 2026

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

  broadinstitute/gatk#9356 · Filter by author C-YONG opened on Apr 8, 2026

• changed BQ permissions - update to documentation needed

  broadinstitute/gatk#9349 · Filter by author bheavner opened on Mar 23, 2026
  5

• Remove BETA tag from VETS tools

  broadinstitute/gatk#9345 · Filter by author jonn-smith opened on Mar 11, 2026

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

  broadinstitute/gatk#9341 · Filter by author EddieLF opened on Mar 3, 2026
  2

• Funcotator - BRCA2 mutation with ambiguous annotation

  broadinstitute/gatk#9339 · Filter by author BarrecaM opened on Feb 27, 2026

• Bitwise OR of a signed byte value

  broadinstitute/gatk#9331 · Filter by author scuniff opened on Feb 17, 2026

• UmiAwareMarkDuplicatesWithMateCigar does not honour --TAGGING_POLICY

  broadinstitute/gatk#9328 · Filter by author DaGaMs opened on Feb 11, 2026

• issue with SelectVariants output file

  broadinstitute/gatk#9326 · Filter by author hddesai opened on Feb 10, 2026

• GATK 4.6.2.0 includes unresolved Critical CVE (CVE-2024-51504)

  broadinstitute/gatk#9325 · Filter by author Zenram opened on Feb 10, 2026

• Resource bundle access denied

  broadinstitute/gatk#9321 · Filter by author sbaross opened on Feb 2, 2026

• Use of java.util.Random to generate seed causes failure

  broadinstitute/gatk#9317 · Filter by author MattWellie opened on Jan 29, 2026
  1

• Funcotator cannot read integer value for start/end position

  broadinstitute/gatk#9309 · Filter by author chstubbe opened on Jan 15, 2026

• Issue with Calculating FS and SOR in GATK VariantAnnotator

  broadinstitute/gatk#9306 · Filter by author Joyjoyjoyc opened on Dec 31, 2025

• CalculateContamination, OutOfRangeException, IllegalArgumentException: log10p: Log10-probability

  broadinstitute/gatk#9298 · Filter by author feiloo opened on Nov 18, 2025

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

  broadinstitute/gatk#9296 · Filter by author Rmulet opened on Oct 31, 2025

• Request for Review of modification to gcnvkernel

  broadinstitute/gatk#9289 · Filter by author ZerryNi opened on Oct 20, 2025
  2

• Clarification about GPU support for GATK

  broadinstitute/gatk#9282 · Filter by author samfux84 opened on Oct 13, 2025
  2