broadinstitute/gatk 4.1.8.1

on GitHub

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)