4.7.0.0

Download release: gatk-4.7.0.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.7.0.0 release:

• Upgraded to HTSJDK 5.0.0 and Picard 3.5.0, bringing full CRAM 3.1 write support and faster BAM/CRAM I/O (#9406, #9216).
• New --output-cram-version option to select the CRAM version (3.0 or 3.1) for CRAM output; default is 3.1 (#9413).
• Updated GKL to 0.9.1, including an optimized implementation of the DRAGEN PDHMM (#9152, #9220).
• Structural variant improvements in SVConcordance, including variant stratification and overlap metrics (#9125).
• Funcotator MANE transcript annotation improvements (#9369, #9226).
• GenotypeGVCFs somatic support extended to use DRAGEN SQ (#9188).
• HaplotypeCaller option to upweight ALT-supporting reads (#9234).

Full list of changes:

• New Tools

  • Added a tool to convert a counts-type file to a depth-type file (#9231).

• HaplotypeCaller

  • Added a command-line option to upweight ALT-supporting reads (#9234).

• Mutect2

  • No changes in this release.

• Joint Calling

  • Extended somatic support in GenotypeGVCFs to use DRAGEN SQ (#9188).

• GenomicsDB

  • No changes in this release.

• Funcotator

  • MANE transcript annotation logic changes (#9369).
  • Additional fixes to MANE transcript selection mode (#9226).
  • Fixed transcript-override functionality (#9214).
  • Fixed documentation links (#9159).

• Mitochondrial pipeline

  • No changes in this release.

• CNV Calling

  • See the new counts-to-depth conversion tool under New Tools (#9231).

• SV Calling

  • Added variant stratification and overlap metrics in SVConcordance (#9125).
  • Check breakpoint distance for each CPX interval and overall in SVConcordance (#9324).
  • Do not strip ECN fields from truth records in SVConcordance (#9161).
  • Improved handling of intersecting groups in SVStratify (#9185).
  • Sort CPX intervals by position in SVAnnotate (#9175).
  • Fixed index outputs from PrintSVEvidence and CollectSVEvidence (#9269).

• Notable Enhancements

  • Added --output-cram-version to control the CRAM output version (3.0/3.1) (#9413).
  • Optimized DRAGEN PDHMM implementation via GKL 0.9.1 (#9152, #9220).

• Bug Fixes

  • (Tool-specific fixes are listed under their respective sections above — Funcotator #9214/#9159, SV #9269/#9161.)

• Miscellaneous Changes

  • Staged the Docker build so a variant without the conda environment can also be built (#9168).
  • Read build artifacts from Google Artifact Registry (GAR) (#9198).
  • Pinned the gcnvkernel dependency for Python 3.10 and other build fixes (#9313).
  • Silenced CodeQL JavaScript/TypeScript errors (#9304).
  • Updated CI job-matrix names so the relevant details appear in the dashboard (#9189).
  • Migrated Maven Central publishing to the Sonatype Central Portal (#9415).

• Documentation

  • No dedicated documentation changes in this release.

• Dependencies

  • HTSJDK 4.3.0 → 5.0.0 and Picard 3.4.0 → 3.5.0 (#9406); earlier in-cycle htsjdk update (#9216).
  • GKL → 0.9.1 (#9220).
  • commons-beanutils 1.9.4 → 1.11.0 (#9201).

New Contributors

• @kockan made their first contribution in #9214
• @ungwudik made their first contribution in #9198
• @VJalili made their first contribution in #9231
• @chirayuharyan made their first contribution in #9220
• @kirschem-roche made their first contribution in #9234

Full Changelog: 4.6.2.0...4.7.0.0