4.1.2.0

Download release: gatk-4.1.2.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.1.2.0 release:

• Two new tools, MethylationTypeCaller and AnalyzeSaturationMutagenesis (see below for descriptions)
• Significant improvements to GENOTYPE_GIVEN_ALLELES mode in Mutect2 and HaplotypeCaller
• Fixed a serious bug in Funcotator that could cause END positions to be wrong for some deletions in MAF output
• Significant updates to the mitochondrial calling pipeline

Full list of changes:

• New Tools

  • MethylationTypeCaller (#5762)
    • Identifies methylated bases from bisulfite sequencing data. Given a bisulfite sequenced, methylation-aware aligned BAM and a reference, it outputs methylation-site coverage to a specified output vcf file.
  • AnalyzeSaturationMutagenesis (#5803)(#5883)
    • Processes reads from a saturation mutagenesis experiment, an experiment that systematically perturbs a mini-gene to ascertain which amino-acid variations are tolerable at each codon of the open reading frame. Its main job is to discover variations from wild-type sequence among the reads, and to summarize the variations observed.

• Mutect2

  • Made significant improvements to GENOTYPE_GIVEN_ALLELES mode in Mutect2 and HaplotypeCaller (#5874). These improvements are described in more detail in #5857
  • CalculateContamination now works much better for very small gene panels (#5873)
  • We now correctly handle inputs with 100% contamination in Mutect2 filtering (#5853)
  • Mutect2 now uses natural logarithms internally (#5858). This does not change any outputs.
  • Minor update to the Mutect2 PON WDL (#5859)

• Funcotator

  • Fixed a serious bug that could cause END positions to be wrong for some deletions in MAF output (#5876)
  • The tool now throws a user error for an AD field with only 1 value in MAF mode (#5860)
  • Added a new filter to FilterFuncotations. For two autosomal recessive genes, MUTYH and ATP7B, homozygous variants and compound heterozygous variants will be tagged and added to the output vcf. (#5843)

• Mitochondrial Calling Pipeline

  • Updated the pipeline for the new Mutect2 filtering scheme and pulled filtering after the liftover and recombining of the VCF. (#5847)
  • Made the subsetting of the WGS bam fast by using PrintReads over just chrM instead of traversing the whole bam for NuMT mates. (#5847)
  • Moved polymorphic NuMTs based on autosomal coverage to a filter (it was an annotation before) (#5847)
  • Added an option to hard filter by VAF (#5847)
  • Bug fix for large input files to the mitochondrial pipeline (we now include the size of the input BAM/CRAM when calculating disk size, when necessary) (#5861)

• Structural Variation Calling Pipeline

  • Bug fix to QNameFinder to handle reads with negative unclipped starts (#5864)

• Miscellaneous Changes

  • Added a --min-fragment-length argument to the FragmentLengthReadFilter (#5886)
  • Added a --spark-verbosity argument to control verbosity of Spark-generated logs (#5825)
  • Added a new WalkerBase abstract class to be used for all built-in walkers (#4964)
  • Exposed transient attributes in the GATKRead API (#5664)
  • Convert more code to use GATKPathSpecifier (#5870) (#5832). This also fixes an InvalidPathException on Windows machines.
  • Fixes to the test suite related to the recent introduction of a codec for Picard interval lists (#5879)
  • Eliminated an error message during the Docker build in Travis logs by creating a directory before copying to it. (#5878)

• Documentation

  • Updated the Mutect2 WDL README with Funcotator information (#5892)
  • Updated a usage example for CreateHadoopBamSplittingIndex (#5898)