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@droazen droazen released this 26 Apr 15:37
· 1374 commits to master since this release
4.0.4.0
7641f53

Highlights of this release include major performance improvements to MarkDuplicatesSpark, better sensitivity and precision in STR (short tandem repeat) contexts for Mutect2, support for a "genotype given alleles" mode in Mutect2, dbSNP support for Funcotator, and several important bug fixes to CombineGVCFs.

As usual, a docker image for this release can be downloaded from https://hub.docker.com/r/broadinstitute/gatk/

Full list of changes in this release:

  • MarkDuplicatesSpark

    • New, optimized version of the tool with greatly improved performance and scalability (#4656)
    • Note that this tool is still marked as beta, and has a number of known issues. The current version is suitable for evaluation/profiling purposes only.

  • Mutect2 improvements

    • Added a GGA (genotype given alleles) mode activated via the --genotyping-mode GENOTYPE_GIVEN_ALLELES and --alleles arguments (#4601)
    • Better sensitivity and precision in STR (short-tandem repeat) contexts (#4690)
    • New, supported Mutect2 NIO-enabled WDL that works in Firecloud (#4710)
    • Better default AF for M2 tumor-normal mode (#4690)
    • Restored explicit PASS (as opposed to empty) filter in Mutect2 (#4644)
    • Fixed Mutect2 failure for germline resource without AF (#4607)
    • Fixed a bug in the Mutect2 WDL bamout where scatters with overlapping assembly regions failed (#4613)
    • Fixed extra filtering args being deactivated in Mutect2 WDL due to typo

  • CombineGVCFs: several important bug fixes

    • ReferenceConfidenceVariantContextMerger fixes for spanning deletions, and use the correct types for the median calculation. (#4680)
    • Handle trailing reference blocks correctly (#4615)
    • Fix and test for calculating intermediate band interval start locations. (#4681)

  • Funcotator

    • Added dbSNP support via a new VcfFuncotationFactory. (#4593)
    • Fixed the refContext annotation. (#4605)
    • Fixed calculation of GC content to be correct. (#4608)
    • Fixes for HG38 exception and better logging. (#4563)
    • Note: only datasource releases 1.2.20180329 and later will work with this version of Funcotator

  • HaplotypeCaller: Fixed a bug that caused the --comp and --input-prior arguments to not be settable by the user (#4703)

  • CNNScoreVariants: Better numerical consistency between python and java, and transpose bug fix (#4652)

  • CNV Tools

    • A new framework to support automated evaluation of GATK CNV (#4276)
    • Enabled zero eigensamples to be specified for CreateReadCountPanelOfNormals (#4502)
    • Exposed maximum chunk size in CNV panel of normals. (#4528)
    • Changed CNV PoN to filter on equality to interval median percentile. (#4503)

  • SV Tools

    • Breakpoint location and type inference unit (#4562)
    • Scaffold local assemblies (#4589)
    • Use the latest version of fermilite jni (#4622)
    • Update sv scripts to only copy a single bam file and index, and respect project parameter (#4646)
    • Various bug fixes (#4670) (#4623)

  • Added GCS (Google Cloud Storage) output support to the following tools: ApplyBQSR, SplitNCigarReads, ClipReads, LeftAlignIndels, RevertBaseQualityScores, and UnmarkDuplicates (#4695) (#4424)

  • Mark the --disable-tool-default-read-filters argument as advanced, and add a warning to its documentation string (#4671)

    • Many tools do not function correctly without their default read filters turned on, so this argument is intended only for advanced users who know what they're doing!

  • ParallelCopyGCSDirectoryIntoHDFSSpark: allow the tool to take a filename glob to subset files to copy (#4624)

  • Picard: updated to version 2.18.2 (#4676)

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