A release which includes major improvements to Mitochondrial calling in Mutect2 as well as bug fixes and improvements:
As always a docker is available here: https://hub.docker.com/r/broadinstitute/gatk/
Mutect2 and HaplotypeCaller changes:
-
Added
--mitochondria-modetoMutect2andFilterMutectCalls. This increases sensitivity and only applies filters that are optimized for mitochondria. A best practices WDL for calling mitochondrial variants on WGS data will be available in the future. (#5193) -
Strand based annotations will use both reads in an overlapping read pair (#5286)
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Realignment filter annotates the VCF with passing and failing read counts (#5328)
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New filters and annotation to support blood biopsy that count and filter based on N's at variant sites (#5317)
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Fixed bug for M2 GGA alleles with zero coverage (#5303)
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Fixed error in genotype given alleles mode when input alleles have genotypes (#5341) #5336
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Add new annotations to bamout to make understanding calls easier (#5215)
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Fixed a typo.
CNV Pipeline:
- Added FilterIntervals to perform annotation-based and count-based filtering in the gCNV pipeline. (#5307) closes #2992 #4558
Spark:
- Removed WellformedReadFilter from CountReadsSpark (#5329)
- Support fasta.gz in GATKSparkTool (#5290) closes #5258
Other:
- CNN variant update models validate scores cleanup training (#5175)
- combine_tracks.wdl supports GISTIC2 conversion (and bugfix) (#5287) closes #5284 #5283
- handle normal reads in validation sample in BasicSomaticValidator (#5322)
GenomicsDB:
- Allow for hdfs and gcs URI's to be passed to GenomicsDB (#5197)
SelectVariants:
SplitNCigarReads:
- Added defensive check to OverhangFixingManager splices for non-reference spanning reads (#5298) closes #5293
- Fixed SplitNCigarReads ArrayIndexOutOfBounds error for reads with long deletions (#5285) closes #5230
Testing: