4.6.2.0

[lbergelson]

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. (Updated references to the funcotator datasets bucket to point to the new google bucket #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 ( Add SVStratify and GroupedSVCluster tools #8990)

• CallableLoci was ported from GATK3 since it is useful in some situations. (Port of CallableLoci from GATK3 #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. (BQSR: avoid throwing an error when read group is missing in the recal table, and some refactoring. #9020)

Full list of changes:

• New Tools

  • Add SVStratify and GroupedSVCluster tools Add SVStratify and GroupedSVCluster tools #8990
  • Port of CallableLoci from GATK3 Add explicit support for headerless SAMRecords to htsjdk #903

• Flow Mode Called

  • Tiny performance improvement Remove unnecessary calculation #9077

• Mutect2+

  • Many small changes to Mutect2 pipelines to support Permutect Lots of little changes to Permutect dataset generation #9094, Optional blacklist VCF to for labeling artifacts in Permutect weak-labeling mode #9136, Small changes to M2 WDL for Permutect #9138

• Funcotator

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

• SV Calling

  • Prioritize het calls when merging clustered SVs 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 BQSR: avoid throwing an error when read group is missing in the recal table, and some refactoring. #9020

• Bug Fixes

  • VariantRecalibrator R script fix so new versions of R work. VariantRecalibrator R script fix for recent R versions. #9046
  • Addressed an edge case in ScoreVariantAnnotations that can occur when one variant type is not present in the input VCF 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 Exclude logback-classic to fix logger configuration warning #9128
  • Close a FeatureReader after use Close a FeatureReader after use #9078

• Miscellaneous Changes

  • Option to retain source IDs on VariantContext merge Retain all source IDs on VariantContext merge + test #9032

• Documentation

  • Update Python compatibility information in README.md Update 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 Testing release #9143
  • Update logback-core from 1.4.14 to 1.5.13 Bump ch.qos.logback:logback-core from 1.4.14 to 1.5.13 #9079
  • Update GenomicsDB Bring in some performance improvements from genomicsdb #9059
  • Update Netty update netty version #9120
  • Exclude bad version of bouncycastle library Uncomment line excluding bad version of bouncycastle library #9129
  • Bump org.apache.commons:commons-vfs2 from 2.9.0 to 2.10.0 Bump org.apache.commons:commons-vfs2 from 2.9.0 to 2.10.0 #9130
  • Update parquet to 1.15.1 Update parquet to 1.15.1 #9144

• Developer Infrastructure

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

Full Changelog: 4.6.1.0...4.6.2.0

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This discussion was created from the release 4.6.2.0.