broadinstitute/gatk 4.2.4.0

4.2.4.0 the log4shell edition

on GitHub

Download release: gatk-4.2.4.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.2.4.0 release:

• Fix a major security bug due to log4j vulnerability. (CVE-2021-44228)
• Improvement to calculation of ExcessHet in joint genotyping. (GenotypeGVCFs, GnarlyGenotyper, ExcessHet).

Full list of changes:

• Funcotator

  • Aligned the Funcotator checkIfAlreadyAnnotated test with the Funcotator engine code. (#7555)

• GenotypeGVCFs / ExcessHet

  • Removed undocumented mid-p correction to p-values in exact test of Hardy-Weinberg equilibrium and updated corresponding tests. We now report the same value as ExcHet in bcftools. Note that previous values of 3.0103 (corresponding to mid-p values of 0.5) will now be 0.0000. (#7394)
  • Updated expected ExcessHet values in integration test resources and added an update toggle to GnarlyGenotyperIntegrationTest.
  • Updated ExcessHet documentation.

• Miscellaneous Changes

  • Delete an unused .gitattributes file which was unintentionally stored in git-lfs and caused an error message to appear sometimes when checking out the repository. (#7594)
  • Remove trailing tab in VariantsToTable output header (#7559)

• Documentation

  • Updated AUTHORS file to remove a contributor's name at their request. (#7580)
  • Remove outdated javadoc line in AssemblyBasedCallerUtils (#7554)

• Dependencies

  • Updated log4j to version 2.13.1 -> 2.16.0 to patch CVE-2021-44228 (#7605)