4.6.2.0

Download release: gatk-4.6.2.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the VERSION release:

• Funcotator Data Location Moved
  We've moved the location that FuncotatorDataSourceDownloader pulls data from because it turned out to be rather expensive to host it there. If you use this in a pipeline we would appreciate it if you updated to the new version. (#9131)

  • Old: https://console.cloud.google.com/storage/browser/broad-public-datasets/funcotator
  • New: https://console.cloud.google.com/storage/browser/broad-public-datasets/funcotator

• New SV Tools There are several new tools to work with SV Data from GATK-SV SVStratify and GroupedSVCluster ( #8990)

• CallableLoci was ported from GATK3 since it is useful in some situations. (#9031)

• New BQSR argument --allow-missing-read-group to work around a rare but annoying issue where BQSR fails if a Read Group is completely filtered from the training data but present at application time. (#9020)

Full list of changes:

• New Tools

  • Add SVStratify and GroupedSVCluster tools #8990
  • Port of CallableLoci from GATK3 #903

• Flow Mode Called

  • Tiny performance improvement #9077

• Mutect2+

  • Many small changes to Mutect2 pipelines to support Permutect #9094, #9136, #9138

• Funcotator

  • Updated references to the funcotator datasets bucket to point to the new google bucket by @KevinCLydon in #9131

• SV Calling

  • Prioritize het calls when merging clustered SVs #9058

• Notable Enhancements

  • BQSR: avoid throwing an error when read group is missing in the recal table, and some refactoring. by @takutosato in #9020

• Bug Fixes

  • VariantRecalibrator R script fix so new versions of R work. #9046
  • Addressed an edge case in ScoreVariantAnnotations that can occur when one variant type is not present in the input VCF #9112
  • Fix an annoying warning by excluding logback-classic #9128
  • Close a FeatureReader after use #9078

• Miscellaneous Changes

  • Option to retain source IDs on VariantContext merge #9032

• Documentation

  • Update Python compatibility information in README.md #9047

• Dependencies
  Many dependencies updated including bug fixes and security patches

  • Update Htsjdk 4.1.3-> 4.2.0 in
  • Update Picard 3.3.0 -> 3.4.0 #9143
  • Update logback-core from 1.4.14 to 1.5.13 #9079
  • Update GenomicsDB #9059
  • Update Netty #9120
  • Exclude bad version of bouncycastle library #9129
  • Bump org.apache.commons:commons-vfs2 from 2.9.0 to 2.10.0 #9130
  • Update parquet to 1.15.1 #9144

• Developer Infrastructure

  • Update upload_artifact in github actions #9061
  • Update gradle sonatype plugin #9133

Full Changelog: 4.6.1.0...4.6.2.0