All pull requests

Pull requests

• Fixing negative gq and pl

  #9455·koncheto-broad opened Oct 13, 2026Collaborator·

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  4

• VAT participant mappings with zygosity [VS-2041]

  #9454·mcovarr opened Oct 10, 2026Collaborator·

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  1

• Fix the step id used to export HELLBENDER_JSON_SERVICE_ACCOUNT_KEY in CI

  #9449·vjroy opened Sep 29, 2026·

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• Update the ubuntu version for the carrot github action because github retired 20.04

  #9448·vjroy opened Sep 29, 2026·

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• Add --genomicsdb-compression to choose GenomicsDBImport's tile codec

  #9447·tfenne opened Sep 29, 2026Contributor·

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  2

• Declare only the header fields ReblockGVCF can write

  #9446·tfenne opened Sep 29, 2026Contributor·

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  2

• Restore WDL validation of scripts/ in CI and fix mutect2_pon.wdl

  #9443·Lorcan7274 opened Sep 21, 2026·

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• Add a pull request template

  #9442·Lorcan7274 opened Sep 21, 2026·

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• Transition from Intel GKL to fgkl - rust based GKL that's faster with broader platform support

  #9441·tfenne opened Sep 18, 2026Contributor·

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• Hold the per-sample read state managers in an array

  #9440·tfenne opened Sep 16, 2026Contributor·

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• Use an ArrayList for the locus iterator's per-sample read states

  #9439·tfenne opened Sep 16, 2026Contributor·

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• Pre-size the per-sequence kmer set in determineNonUniqueKmers

  #9438·tfenne opened Sep 16, 2026Contributor·

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  1

• Replace boxed Integer caches in SAMRecordToGATKReadAdapter with primitives

  #9437·tfenne opened Sep 16, 2026Contributor·

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• Cache Haplotype.hashCode

  #9436·tfenne opened Sep 16, 2026Contributor·

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• Stop installing the Intel GKL inflater/deflater; use HTSJDK's libdeflate-backed defaults

  #9434·tfenne opened Sep 15, 2026Contributor·1 of 2 tasks·

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  1

• Add a windowed max-depth downsampler for assembly-region walkers (--max-effective-depth)

  #9433·tfenne opened Sep 15, 2026Contributor·

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  13

• TSPS-1069 Get EvaluateGenotypingPerformance Tool merged into master

  #9431·jsotobroad opened Sep 14, 2026Contributor·

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  7

• [DRAFT] Pin Alpine's python3 to 3.12 instead of cloud-sdk's bundled python3.14 [VS-2004]

  #9425·nalinigans opened Sep 1, 2026Collaborator·

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  1

• Bump cloud-sdk base image, 524.0.0 no longer exists [VS-2002]

  #9423·nalinigans opened Sep 1, 2026Collaborator·

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• Allow building and packaging GATK outside of a git clone

  #9420·BenjaminDEMAILLE opened Aug 26, 2026·

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• Make gcnvkernel work with current PyMC, PyTensor and NumPy

  #9418·BenjaminDEMAILLE opened Aug 26, 2026·

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• Gentle refactoring of ActivityProfile code and new somatic ActivityProfile for Mutect2

  #9391·davidbenjamin opened Jun 26, 2026Contributor·

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  1

  

• Add some rare variant mode docs [VS-1813]

  #9385·mcovarr opened Jun 9, 2026Collaborator·

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• Native Apple Silicon (arm64) support for GATK

  #9384·BenjaminDEMAILLE opened Jun 6, 2026·

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  3

• Vs 1813

  #9375·koncheto-broad opened May 15, 2026Collaborator·

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  8