4.6.1.0 #9027
lbergelson
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4.6.1.0
#9027
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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:
CNNScoreVariants
has been replaced byNVScoreVariants
, a rewritten and modernized version. The python code for this tool was written by members of NVIDIA Genomics Research.Funcotator
argument--prefer-mane-transcripts
which improves transcript selection and lays groundwork for upcoming improvements.--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 withSelectVariants
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)
New Tools
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)VcfComparator
(Adds VcfComparator tool #8933, Updates to VcfComparator #8973)Joint Calling GVS
GenomicsDB
Funcotator
SV Calling
Flow Based Calling
Miscellaneous Features
Documentation
Refactoring
Tests
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)
build.gradle
to use of features like consuming publishes Bills of Materials (BOMs)This discussion was created from the release 4.6.1.0.
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