broadinstitute/gatk 4.1.4.0

on GitHub

Download release: gatk-4.1.4.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.1.4.0 release:

• Major improvements and fixes to Mutect2, including more intelligent handling of paired reads during genotyping and better filtering.

• Important bug fixes to HaplotypeCaller, the joint calling pipeline, and Funcotator

• Beta support for building/testing on Java 11 (#6119) (#6145)

  • We encourage you to try this out and give us feedback!

Full list of changes:

• New Tools

  • AlleleFrequencyQC: a QC tool that uses VariantEval to bin variants in 1000 Genomes by allele frequency. For each bin, we compare the expected allele frequency from 1000 Genomes with the observed allele frequency in the input VCF. This was designed with arrays in mind, as a way to discover potential bugs in our pipeline. #6039)

• Mutect2

  • Mutect2 genotyping now forces paired reads to support the same haplotype (#5831)
  • New FilterAlignmentArtifacts now realigns a locally-assembled unitig of all variant read pairs (#6143)
  • Fixed a Mutect2 bug that overfiltered by one variant (#6101)
  • Fixed a small gene panel edge case for CalculateContamination (#6137)
  • Fixed a small gene panel edge case in orientation bias filter (#6141)
  • Unified the NIO and non-NIO M2 WDLs (call-caching will now work on Terra) (#6108)
  • Updated Mutect2 pon WDL to WDL 1.0 (#6187)
  • Removed Oncotator from the M2 WDL (Funcotator is still there) (#6144)
  • Fixed an issue in the M2 WDL that could cause the Funcotate task to be ignored by tools such as dxWDL (#6077)
  • Some miscellaneous code refactoring/improvements (#6184) (#6136) (#6107) (#6159)

• HaplotypeCaller

  • HaplotypeCaller now force-calls like Mutect2: the -genotyping-mode GENOTYPE_GIVEN_ALLELES argument is gone (now you only need to specify --alleles force-calls.vcf) and alleles are now force-called in addition to any other alleles (#6090)
  • Renamed --output-mode EMIT_ALL_SITES to --output-mode EMIT_ALL_ACTIVE_SITES, and clarified the documentation for the argument (#6181)
  • Fixed a rare bug in the genotyping engine where it could emit untrimmed alleles for SNP sites (#6044)
  • Fixed some sources of non-determinism in the HaplotypeCaller that in rare cases could cause the output to vary slightly given the same inputs (#6195) (#6104)
  • Deleted the old exact AF calculation model (#6099)

• Joint Calling

  • Fixed a regression in GATK 4.1.3.0 that caused us to not emit the AS_QD annotation when running a joint calling pipeline with CombineGVCFs (GenomicsDB was unaffected) (#6168)
  • Fixed allele-specific annotation array length issues when alleles are subset in tools such as GenotypeGVCFs (#6079)
  • Changed AS_RankSum outputs to "." for missing values rather than "nul" (#6079)

• Funcotator

  • Fixed a bug that caused Funcotator to outputs fields in wrong order in some cases when writing a VCF (#6178)
    • Specifically, Funcotator would output functation fields in the wrong order when there was more than 1 site in a VCF data source with the exact same position and alleles and it matched one of the variants being annotated

• Mitochondrial pipeline

  • Renamed the output vcf with the name of the sample and supplied a default value for autosomal_median_coverage (meaning you'll now get the NuMT filter even if you don't provide the actual autosomal coverage) (#6160)

• Miscellaneous Changes

  • Beta support for building/testing on Java 11 (#6119) (#6145)
  • UpdateVCFSequenceDictionary now supports replacing an invalid sequence dictionary in a VCF (#6140)
  • CountFalsePositives now requires an intervals file (#6120)
  • AnalyzeSaturationMutagenesis: use supplementary alignments to identify large deletions (#6092)
  • AnalyzeSaturationMutagenesis: an insert at the start codon is not in the ORF (#6121)
  • Added a check for null sequence dictionaries in the dictionary validation code (#6147)
  • Update SV Spark pipeline example shell scripts saving results to GCS (#6114)
  • Update public key for installing R in docker (#6116)
  • Log exceptions during deletion on JVM exit instead of throwing (#6125)
  • Don't fail the build if we're in a git worktree folder (#6169)
  • Free a bit of memory fir the test suite by disabling mysql and postgress on travis (#6085)
  • Delete bogus index files for queryname sorted CRAMs. (#6149)
  • Cleanup GenomicsDB debugging test output (#6089)

• Documentation

  • Fixed mitochondria mode documentation in FilterMutectCalls (#6174)

• Dependencies

  • Updated HTSJDK to 2.20.3 (#6126)
  • Updated Picard to 2.21.1 (#6205)
  • Updated google-cloud-nio to 0.107.0 (#6042)
  • Updated Gradle to 5.6 (#6106)