github broadinstitute/gatk 4.0.8.1

latest releases: 4.5.0.0, after_master_merge, before_master_merge...
5 years ago

This is a small bug fix release to fix an issue with unpaired reads in Mutect2, as well as small fixes and improvements to Funcotator, FilterVariantTranches, and MarkDuplicatesSpark.

As usual, a docker image for this release can be downloaded from https://hub.docker.com/r/broadinstitute/gatk/

Full list of changes in this release:

  • Mutect2: Fixed a "Cannot get mate information for an unpaired read" error that could occur with certain datasets containing unpaired reads that pass all the M2 read filters and show evidence of a SNV (#5121)

  • Funcotator:

    • Fixes to the splice site logic. (#5106)
      • Funcotator now ignores leading indel bases when checking if variants are within the splice site boundaries (eg. if a leading base in an indel, which is preserved between the reference and alternate alleles, is within the splice site boundary but the bases that have been changed are NOT, then the variant is now correctly labeled as NOT a splice site).
    • Populate the DB SNP validation status field properly (#5046)
      • Funcotator will now populate the MAF DB SNP Validation status field with proper values (e.g. "by1000genomes") instead of boolean value (e.g. "TRUE")
      • Funcotator now handles multiple records in a VCF funcotation factory that have the same pos, ref, and alt combination, even if equivalent and not exact matches.
  • FilterVariantTranches:

    • Add an --invalidate-previous-filters argument to remove old filters left over from previous runs (off by default) (#5042)
    • Add --snp-tranche and --indel-tranche arguments to replace the previous --tranche argument (#5042)
  • Updated MarkDuplicatesSpark scoring and comparison code to reflect changes in Picard (#5023)

    • Updated the scoring code to no longer take into account the unclipped start position of mismatching reads. Also changed the score to be a double packed short value in order to better reflect Picard scoring code.
  • Other Changes:

    • Added new IOUtils.isHDF5File() utility method (#5082)
    • Add jitpack support for building GATK snapshots (#5056)
    • Fixed broken link in Travis to docker test failure reports (#5108)

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