broadinstitute/gatk 4.1.7.0

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Download release: gatk-4.1.7.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.1.7.0 release:

• Added allele-specific filtering to the mitochondrial pipeline.

  • Allele-specific filtering is important for mitochondrial calling because there are many more multi-allelic sites than in the germline autosome.

• A fix for the frequently-encountered "Smith-Waterman alignment failure" error in HaplotypeCaller and Mutect2

• Initial support for http(s) paths for BAM inputs, including signed urls

• A new tool, DownsampleByDuplicateSet, to randomly sample a fraction of duplicate sets from an input bam sorted by UMI

Full list of changes:

• New Tools

  • DownsampleByDuplicateSet: a new tool to randomly sample a fraction of an input bam sorted by UMI. (#6512)
    • Given a bam grouped by unique molecular identifier (UMI), this tool drops a specified fraction of duplicate sets and returns a new bam.
    • A duplicate set refers to a group of reads whose fragments start and end at the same genomic coordinate and share the same UMI.
    • The input bam must first be sorted by UMI using FGBio GroupReadsByUmi.
    • Use this tool to create, for instance, an insilico mixture of duplex-sequenced samples to simulate tumor subclones.

• HaplotypeCaller/Mutect2

  • Fixed a regression in HaplotypeCaller and Mutect2 where alt haplotypes with a deletion at the end of the padded region caused exceptions (#6544)
    • This bug produced error messages like the following: "Smith-Waterman alignment failure. Cigar = 275M with reference length 275 but expecting reference length of 303"
  • Fixed an ArrayIndexOutOfBoundsException in GenotypeUtils.computeDiploidGenotypeCounts() caused by mistakenly assuming ploidy two for no-calls (#6563)
  • Added more control over scattering in the Mutect2 PON WDL to allow arbitrarily fine scattering, reducing the memory required for downstream runs of GenomicsDBImport (#6527)
  • Invert --correct-overlapping-quality argument in HaplotypeCaller to --do-not-correct-overlapping-quality (#6528)

• Mitochondrial Pipeline

  • Added allele-specific filtering to the mitochondrial pipeline (#6399)
    • Allele-specific filtering is important for mitochondria because there are many more multi-allelic sites than in the germline autosome and therefore, downstream tools have access to more of the good allele data.
    • These Mutect2 filters used in the MT pipeline are now allele-specific: weak_evidence, base_qual, map_qual, duplicate, strand_bias, strand_artifact, position, contamination, and low_allele_frac.
    • They are added to the AS_FilterStatus annotation in the INFO field.
    • The numt_chimera and numt_novel filters have been replaced by the possible_numt filter.
    • Two new filtering tools have been added: NuMTFilterTool for the possible_numt filter and MTLowHeteroplasmyFilterTool for the mt_many_low_hets filter, both of which are allele-specific.
    • The --split-multi-allelics option of the LeftAlignAndTrimVariants tool now splits the annotations in the FORMAT and INFO fields that are of type A and R (allele-specific, and allele-specific with reference).
    • The VariantFiltration tool now has an --apply-allele-specific-filters option that will apply masks at the allele level. Before this addition, sites that should not be masked, but had deletions that spanned a masked site would have been masked. Now, if this option is specified, only the alleles spanning the masked site will be masked.

• GATK Engine

  • Added initial support for http(s) paths for BAM inputs, including signed urls (#6526)

• Miscellaneous Changes

  • Exposed maximum copy ratio and point size for CNV plotting tools (#6482)
  • Decreased an epsilon value in VariantRecalibrator so that our production exome joint genotyping tests pass (#6534)
  • Migrated reference arguments and downstream code to GATKPathSpecifier (#6524)
  • Removed obsolete isCompatibleWithSparkBroadcast() method. (#6523)

• Documentation

  • Cleaned up the handling of some missing values in auto-generated GATK tool documentation (#6565)
    • Now docs won't include null, "", or [] in the default value list.
  • Added a README for the CNN variant scoring workflow, and added an input JSON for Mutect2 workflow files located in GCS buckets (#6542)
  • Fixed a typo in a ploidy prior example in the docs for DetermineGermlineContigPloidy (#6531)