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@droazen droazen released this 19 Aug 00:08
· 354 commits to master since this release
4.2.2.0
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Learn about vigilant mode.

Download release: gatk-4.2.2.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.2.2.0 release:

  • The ReblockGVCF tool is now out of beta with several important improvements. This tool can be used to postprocess HaplotypeCaller GVCFs to decrease filesize.

  • FilterMutectCalls now has a --microbial-mode argument that sets filters to defaults appropriate for microbial calling

  • Important bug fixes to CalibrateDragstrModel and Funcotator

Full list of changes:

  • New Tools

    • ShiftFasta: create a fasta with the bases shifted by an offset (#6694)

  • ReblockGVCF

    • ReblockGVCF is now out of beta (#7419)
    • Improved ReblockGVCF output to eliminate overlapping reference blocks and reference gaps following trimmed deletions (#7122)
    • Fixed bugs associated with input no-call genotypes and fixed an off-by-one error at contig starts (#7404)
    • Fixed an error on ref blocks with missing DPs (if --floor-blocks arg is not provided); fixed rare cases where spanning deletion (*) allele is incorrectly modified (#7400)

  • Mutect2

    • FilterMutectCalls: added a --microbial-mode argument that sets filters to defaults appropriate for microbial calling (#6694)

  • ValidateVariants

    • Added an optional argument to check for GVCF reference blocks overlapping variants or other reference blocks (#7405)

  • DRAGEN-GATK

    • Fixed a thread safety issue in CalibrateDragstrModel that could cause intermittent ArrayIndexOutOfBoundsExceptions (#7417)
    • Added documentation for ComposeSTRTableFile (#7409)

  • Funcotator

    • Fixed an issue where the Match_Norm_Seq_Allele1 and Match_Norm_Seq_Allele2 fields were not being populated in MAF output (#7422)

  • Mitochondrial pipeline

    • Removed calls to FilterNuMTs and FilterLowHetSites, which are no longer being used (#7325)

  • CNV Calling

    • Fixed a bug resulting from prefix strings of less than 3 characters when creating temporary files in GermlineCNVCaller and improved documentation of corresponding utility methods. (#7411)

  • Documentation

    • Fixed an argument name typo in the CombineGVCFs docs (#7413)
    • Fixed the wording of a comment in MultiVariantDataSource (#7388)
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