4.6.1.0

[lbergelson]

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• CNNScoreVariants has been replaced by NVScoreVariants, a rewritten and modernized version.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 (Port of nvscorevariants into GATK, with a basic tool frontend #8004, Mark NVScoreVariants as a beta feature #9010, Remove CNNScoreVariants, CNNVariantTrain, and CNNVariantWriteTensors #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  • CNNScore variants has been replaced by NVScoreVariants, scripts that use it should be updated to use NVScoreVariants instead.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 (Create tool for producing genomic regions (as a BED file) #7159, Issue #7159 Create tool for producing genomic regions (as a BED file) #8942)
  • New tool for internal use VcfComparator (Adds VcfComparator tool #8933, Updates to VcfComparator #8973)

• Joint Calling GVS

  • Adds QD and AS_QD emission from VariantAnnotator on GVS input (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 (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 )(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 (Handle CTX_PP/QQ and CTX_PQ/QP CPX_TYPE values in SVConcordance #8885)
  • Complex SV intervals support by @mwalker174 (Complex SV intervals support #8521)
  • Require both overlap and breakend proximity for depth-only SV clustering (Require both overlap and breakend proximity for depth-only SV clustering #8962)

• Flow Based Calling

  • Modified HaplotypeBasedVariantRecaller to support non-flow reads (Modified HaplotypeBasedVariantRecaller to support non-flow reads #8896)
  • FlowFeatureMapper: X_FILTERED_COUNT semantics adjusted and documented more accurately (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 (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 (Clarify in the README which git lfs files are required to build GATK #8914)
  • Add docs about citing GATK (Add docs about citing GATK #8947)
  • Update Mutect2.java Documentation (Update Mutect2.java Documentation #8999)
  • Add more detailed conda setup instructions to the GATK README (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 (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 (Swapped mito mode in Mutect to use the mode argument utils #8986)

• Tests

  • Adding a test to capture an expected edge case in Reblocking (Adding a test to capture an expected edge case in Reblocking #8928)
  • Update the large CRAM files to v3.0 (Update the large CRAM files to v3.0. #8832)
  • Update CRAM detector output files (Update CRAM detector output files. #8971)
  • Add dependency submission workflow so we can monitor vulnerabilities (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. (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 (Update docker base #9005)

  • Updates to java build and dependencies (Update gradle and build.gradle #8998, Additional Dependency updates #9006, Use jetty bom to enforce uniform jetty versions #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 (Update hdf5-java-bindings to version 1.2.0-hdf5_2.11.0, which removes log4j 1.x #8908)

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This discussion was created from the release 4.6.1.0.