4.6.1.0

Download release: gatk-4.6.1.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.6.1.0 release:

• Modernize the aging Conda environment with up to date python dependencies. All the python tools have been updated appropriately. This will enable easier integration of new machine learning tools.
  • If you use python tools outside of the docker, you must rebuild your conda environment for this release
• CNNScoreVariants has been replaced by NVScoreVariants, a rewritten and modernized version. The python code for this tool was written by members of NVIDIA Genomics Research.
  • Thank you Babak Zamirai, Ankit Sethia, Mehrzad Samadi, George Vacek and the whole NVIDIA genomics team!
  • This GATK blog post has more of the story from when we first made the tool available for testing.
• New Funcotator argument --prefer-mane-transcripts which improves transcript selection and lays groundwork for upcoming improvements.
• New argument --variant-output-filtering which lets you restrict output variants based on the input intervals. This replaces and imrpoves on --only-output-calls-starting-in-interval and works with SelectVariants and other VariantWalkers. This is useful to prevent duplicating variants when splitting an input VCF into multiple shards.

Full list of changes:

• CNNScoreVariants -> NVScoreVariants (#8004, #9010, #9009)

  • CNNScore variants has been replaced by NVScoreVariants, scripts that use it should be updated to use NVScoreVariants instead.
  • The training tools (CNNVariantTrain, CNNVariantWriteTensors)have been removed. If you need to retrain the model for your data type you should continue to use GATK 4.6.0.0. New training tools are in development to work alongside NVScoreVariants and will be added in subsequent releases.

• New Tools

  • New tool GtfToBed to convert Gencode GTF files to BED files (#7159, #8942)
  • New tool for internal use VcfComparator (#8933, #8973)

• Joint Calling GVS

  • Adds QD and AS_QD emission from VariantAnnotator on GVS input (#8978)

• GenomicsDB

  • Switch to logging a warning instead of an exception for intervals in query that were not part of GenomicsDBImport (#8987)

• Funcotator

  • Added a '--prefer-mane-transcripts' mode that enforces MANE_Select tagged Gencode transcripts where possible )(#9012)

• SV Calling

  • Handle CTX_PP/QQ and CTX_PQ/QP CPX_TYPE values inSVConcordance (#8885)
  • Complex SV intervals support by @mwalker174 (#8521)
  • Require both overlap and breakend proximity for depth-only SV clustering (#8962)

• Flow Based Calling

  • Modified HaplotypeBasedVariantRecaller to support non-flow reads (#8896)
  • FlowFeatureMapper: X_FILTERED_COUNT semantics adjusted and documented more accurately (#8894)
  • Changes to flow arguments in haplotype caller from Picard (see Picard release notes

• Miscellaneous Features

  • Added a check for whether files can be created and executed within the configured tmp-dir (#8951)

• Documentation

  • Clarify in the README which git lfs files are required to build GATK (#8914)
  • Add docs about citing GATK (#8947)
  • Update Mutect2.java Documentation (#8999)
  • Add more detailed conda setup instructions to the GATK README (#9001)
  • Adding small warning messages to not to feed any GVCF files to these tools (#9008)

• Refactoring

  • Swapped mito mode in Mutect to use the mode argument utils (#8986)

• Tests

  • Adding a test to capture an expected edge case in Reblocking (#8928)
  • Update the large CRAM files to v3.0 (#8832)
  • Update CRAM detector output files (#8971)
  • Add dependency submission workflow so we can monitor vulnerabilities (#9002)

• Dependencies
  Updating dependencies to make use of modern frameworks with fewer vulnerabilities was a focus of this release.

  • Updated Python and PyMC, removed TensorFlow, and added PyTorch in conda environment. (#8561)

  • Rebuild gatk-base docker image (3.3.1) in order to pull in recent patches (#9005)

  • Updates to java build and dependencies (#8998, #9006, #9016)

    • Update to the Gralde 8.10.2
    • Improvements to build.gradle to use of features like consuming publishes Bills of Materials (BOMs)
    • Update many direct and transitive java dependencies to fix security vulnerabilities.
    • Update Htsjdk 4.1.1 to 4.1.3
    • Update Picard 3.2.0 to 3.3.0
    • Update hdf5-java-bindings to version 1.2.0-hdf5_2.11.0 (#8908)