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@droazen droazen released this 20 Jul 21:14
· 547 commits to master since this release
4.1.8.1
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Download release: gatk-4.1.8.1.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.1.8.1 release:

  • This is a minor point release intended primarily to push out a needed enhancement to the Mutect2 pipeline.

  • This release also introduces a new framework for the auto-generation of WDLs for GATK/Picard tools. Over the next several GATK releases, we intend to hook GATK/Picard tools up to the new WDL generator, with the ultimate goal of having WDLs automatically published for all tools with each release.

Full list of changes:

  • Mutect2

    • We now allow for the passing of additional arguments to GetPileupSummaries from the Mutect2 WDL (#6713)

  • GATK Engine

    • Added a new framework for the auto-generation of WDLs for GATK/Picard tools (#6504)
      • Over the next several GATK releases, we intend to hook GATK/Picard tools up to the new WDL generator, with the ultimate goal of having WDLs automatically published for all tools with each release

  • Bug Fixes

    • Fixed an error (reported in #6664) when trying to read .vcf/.tbi files located in a path that contains spaces in the name (#6702)

  • Miscellaneous Changes

    • Removed a few GATK classes that are redundant with Picard classes. (#6678)

  • Documentation

    • Added instructions for running Spark tools in LOCAL mode to the README (#6682)
    • Removed documentation reference to a GATK 3.x annotation that no longer exists (#6679)

  • Dependencies

    • Updated HTSJDK to 2.23.0 (#6702)
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