broadinstitute/gatk 4.0.2.0

on GitHub

This is a small release that includes a new Beta tool, a port of VariantAnnotator from Gatk3, as well as some bug fixes and other improvements. Mutect2 is no longer beta.

• Mutect2 and FilterMutectCalls are now no longer beta! (#4384)

• new tool VariantAnnotator (#3803):

  • ported tool from GATK3
  • first beta release

• Spark Improvements:

  • fix a major performance regression that harmed performance of spark tools (#4428)
  • SortReadFileSpark renamed -> SortSamSpark (#4442)
  • minor improvements to Kryo registration (#4451)

• new CNV Tumor only WDL (#4414)

• Viterbi segmentation and segment quality calculation for gcnvkernel (#4335)

• Other Bug Fixes and Improvements:

  • update to latest GKL, improves performance of GZIP level 2 compression (#4379)
  • CalculateGenotypePosteriors fixed bug that caused duplicates in the output VCF as well as several other issues (#4352, #4431)
  • Display a more prominent warning message for Beta and Experimental tools. (#4429)
  • non-zero Picard tool exit codes now cause a non-zero exit from gatk (#4437)
  • removed support for deprecated Google Reference API (#4266)
  • Improve evidence info dumps and SV pipeline management (#4385)
  • oncotator docker uses default docker if not specified (#4394)
  • Added check for non-finite copy ratios in ModelSegments pipeline. (#4292)
  • make FASTQ reader remove phred bias from quals (#4415)