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4.0.2.0
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@lbergelson lbergelson released this 27 Feb 03:27
· 1473 commits to master since this release
4.0.2.0
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lbergelson Louis Bergelson
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Learn about vigilant mode.
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Learn about vigilant mode.

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)
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