4.0.5.1

This is primarily a bug fix release to fix a crash in the help system (#4875). The issue was that tools that use annotations (which includes Mutect2, HaplotypeCaller, GenotypeGVCFs, CombineGVCFs, and VariantAnnotator) would crash when trying to print their help text. This could be triggered by running with an explicit --help, or by typing an invalid tool command line.

This release also brings in some improvements to Funcotator, including a new mode to output annotations for all transcripts.

As usual, a docker image for this release can be downloaded from https://hub.docker.com/r/broadinstitute/gatk/

Full list of changes in this release:

• Fix crash when displaying help text for tools that use annotations (#4876)
• Funcotator improvements (#4838) (#4870)
  • Added ALL mode for transcript selection (--transcript-selection-mode ALL) which will output full annotation fields for all transcripts
  • IGR annotation are no longer reported if there are any transcripts that would result in a non-IGR annotation for a given variant
  • VCF Datasources now have to match both the alt and ref alleles to be added as annotations to a variant
  • Added the --allow-hg19-gencode-b37-contig-matching-override flag to allow for even more permissive matching contig names between B37 and HG19 references (primarily designed to be used in development)
  • Updated the experimental Funcotator WDL to work properly in cromwell
  • Refactored internals of Funcotator to use FuncotationMap objects to store annotations
  • Additional tests to ensure VCF and MAF protein change strings are equivalent
  • Other minor internal bugfixes for testing
• Fix to the Oncotator command line in the Mutect2 WDL (#4862)
• Removed unsupported Mutect2 WDLs (these now live on Firecloud) (#4836)