broadinstitute/gatk 4.2.2.0

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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)