Some important fixes in this release include a new version of GenomicsDB with a fix for the stack overflow seen when using large interval lists, and an updated Docker image with a fix for the missing R/ggplot2 dependencies.
As usual, a docker image for this release can be downloaded from https://hub.docker.com/r/broadinstitute/gatk/.
Docker
- Restore missing R/ggplot2 dependencies on the Docker image. [#5040 (https://github.com//pull/5040)
GenomicsDB
- Fix GenomicsDBImport stack overflow when using large number of intervals #4997
Mutect2
- Don't use very short stubs of clipped reads for genotyping #5057
- Add maxRetries to runtime in M2 WDLs #5049
- Fix an edge case bug in PalindromeArtifactReadTransformer #5038
- Make orientation bias filtering default to true #5019
- Added option for ValidateBasicSomaticShortMutations to output a vcf #4999
- Add Mutect2 PalindromeArtifactReadTransformer to hard clip inverted tandem repeats insertion artifacts #4998
- Making MAF become the output of Funcotator in M2 WDL and multiple transcript fix. #4941
CNV Tools
- Exposed ability to blacklist intervals in CNV WDLs. #5027
- Added output of IGV-compatible .seg files to ModelSegments. #5048
Structural Variants
- Add BreakpointEvidence filter based on classifier #4769
- Address more edge cases in assembly alignments #5044
- Refactor AssemblyContigAlignmentsConfigPicker #4971
- Fix an edge case in assembly contig alignment picker where no good mappings to canonical mappings exist #5005
- Trim down ref bases for CPX variants #4970
Funcotator
- VCF Funcotation Factory will recognize equivalent alleles (even when not exact) #4977
Other