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4.2.4.0 the log4shell edition
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@lbergelson lbergelson released this 15 Dec 19:33
· 331 commits to master since this release
4.2.4.0
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lbergelson Louis Bergelson
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Learn about vigilant mode.
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Learn about vigilant mode.

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    • Remove outdated javadoc line in AssemblyBasedCallerUtils (#7554)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

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