19 Pull requests merged by 6 people

• Fix ploidy compatibility with VDS intermediate_resume_point [VS-1633]

  #9252 merged Aug 14, 2025

• Handle incrementally extracted vet and ref_ranges Avros [VS-1633]

  #9250 merged Aug 13, 2025

• Foxrot Avro extract and VDS-making fixes [VS-1633]

  #9249 merged Aug 13, 2025

• Fix more superpartition table name matches [VS-1631]

  #9247 merged Aug 11, 2025

• Gg vs 1719 better ref support

  #9242 merged Aug 7, 2025

• VAT duplicate handling investigation [VS-1683]

  #9244 merged Aug 7, 2025

• Minor doc update for updated Foxtrot manifest [VS-1721]

  #9245 merged Aug 7, 2025

• Adding Foxtrot VDS merge details [VS-1692]

  #9246 merged Aug 7, 2025

• VS-1509. Get WDL validation working again.

  #9237 merged Jul 30, 2025

• Prepare for GVS release 0.6.4 [VS-1718]

  #9240 merged Jul 29, 2025

• Cost estimates and the fixes they inspired [VS-1674] [VS-1710] [VS-1712]

  #9233 merged Jul 29, 2025

• Updated GKL version to 0.9.1

  #9220 merged Jul 29, 2025

• WDL for the dogs (and cats) [VS-1691]

  #9219 merged Jul 29, 2025

• VS-1716. Have Extract check for the existence of ploidy table

  #9236 merged Jul 28, 2025

• Adds a tool for converting a counts type file to a depth type file.

  #9231 merged Jul 28, 2025

• Increase Default Disk for MergeVCFs task for FoxTrot Callset

  #9235 merged Jul 23, 2025

• Improved handling of intersecting groups in SVStratify

  #9185 merged Jul 23, 2025

• More fixes to MANE transcript selection mode

  #9226 merged Jul 22, 2025

• Ignore weirdly named vets tables [VS-1711]

  #9232 merged Jul 21, 2025

2 Pull requests opened by 2 people

• Add command line option to HaplotypeCaller for upweighting ALT-suppor…

  #9234 opened Jul 21, 2025

• Update MendelianViolation . Fix java.lang.IndexOutOfBoundsException: when a genotype is haploid.

  #9241 opened Jul 30, 2025

1 Issue closed by 1 person

• Failure to genotype large deletions (125bp+) in Mutect2, using --alleles option

  #9239 closed Jul 31, 2025

4 Issues opened by 4 people

• DetermineGermlineContigPloidy - Badly formed genome unclippedLoc

  #9251 opened Aug 14, 2025

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

  #9248 opened Aug 12, 2025

• Feasibility of Tumor-Only Workflow for cfDNA with Mutect2

  #9243 opened Aug 1, 2025

• Why CombineGVCFs so stupid to read the whole g.vcf when giving --intervals?

  #9238 opened Jul 29, 2025

5 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• BQSR: restore ability to specify custom covariates and to disable standard covariates. (Take 2)

  #9206 commented on Jul 28, 2025 • 41 new comments

• GenotypeGVCFs stuck at Starting traversal for coulple of days!!!

  #7866 commented on Jul 31, 2025 • 0 new comments

• bug: Mutect2 doesn't respect provided --sequence-dictionary

  #9208 commented on Jul 31, 2025 • 0 new comments

• LeftAlignIndels Alignments added out of order issue when reads are fed in coordinate sorted order.

  #8975 commented on Aug 1, 2025 • 0 new comments

• Funcotator - Google bucket inaccessible

  #9167 commented on Aug 13, 2025 • 0 new comments