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v1.0.4

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@epiercehoffman epiercehoffman released this 22 May 17:40
· 100 commits to main since this release
v1.0.4
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Learn about vigilant mode.

What's Changed

Critical

The AnnotateVcf workflow configuration in Terra has been corrected to take the filtered VCF as input.

  • If you have processed a cohort with GATK-SV in Terra and you have run FilterGenotypes, you should be aware that the AnnotateVcf output may not be filtered.
  • You can tell whether a VCF has been through filtering by looking for the NCR INFO field in the header - if it’s there, FilterGenotypes has been applied.
  • To address this, copy the updated AnnotateVcf workflow from the featured workspace to get the new input configuration, and update the gatk_docker in Workspace Data to match the featured workspace.

Bug fixes

  • Update GATK docker with CPX interval sorting fix for SVAnnotate
  • CPU configuration workaround for RealignSoftClippedReads
  • Enable non-existent INFO/EVIDENCE fields in input VCF for breakpoint overlap filtering in ResolveComplexVariants

Miscellaneous

  • Remove hail-based VCF merging
  • Update website regarding GATK forum

Full Changelog: v1.0.3...v1.0.4

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