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4.0.11.0
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@lbergelson lbergelson released this 23 Oct 20:22
· 1130 commits to master since this release
4.0.11.0
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lbergelson Louis Bergelson
GPG key ID: CDB73EA73CD9CF1E
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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-mode to Mutect2 and FilterMutectCalls. 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)

  • Realignment filter annotates the VCF with passing and failing read counts (#5328)

  • New filters and annotation to support blood biopsy that count and filter based on N's at variant sites (#5317)

  • Fixed bug for M2 GGA alleles with zero coverage (#5303)

  • Fixed error in genotype given alleles mode when input alleles have genotypes (#5341) #5336

  • Add new annotations to bamout to make understanding calls easier (#5215)

  • 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:

  • Enable SelectVariants to drop specific annotation fields from output vcf. (#5254) closes #5235

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:

  • Added a toggle to update the expected outputs in HaplotypeCallerIntegrationTest (#5324)
  • Added a new servicekey.json for travis (#5308) closes #5305
  • Added full-sized B37 and HG38 references to our large test data (#5309) closes #5111
  • Added in new data sources for funcotator testing. (#5296)
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