broadinstitute/gatk 4.2.3.0

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Download release: gatk-4.2.3.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.2.3.0 release:

• Notable bug fixes for Mutect2 and Funcotator

• Support in CombineGVCFs and GenotypeGVCFs for "reblocked" GVCFs as produced by the ReblockGVCF tool. Reblocked GVCFs have a significantly reduced storage footprint.

• More control over the Smith-Waterman parameters in HaplotypeCaller and Mutect2

• A new Fragment Allele Depth (FAD) variant annotation similar to the AD annotation except that allele support is considered per read pair, not per individual read

• GenomicsDB bug fixes and enhancements

Full list of changes:

• HaplotypeCaller/Mutect2

  • Fixed a bug where Mutect2 failed to filter germline variants with alternate representations (#7103)
    • This caused variants with alternative representations in gnomAD to not be recognized as being the same as called variants in some cases. This resulted in variants that were called and not filtered, but they should have been filtered by "germline".
  • Exposed Smith-Waterman parameters as tool arguments in HaplotypeCaller, Mutect2, and FilterAlignmentArtifacts. (#6885)
    • Enables use of alternative parameters for different event representation (e.g. three consecutive SNPs instead of two small indels)
  • Can now specify the Smith-Waterman implementation in FilterAlignmentArtifacts (#7105)
  • Added a --debug-assembly-variants-out diagnostic option to output a side VCF with variants detected by assembly for HaplotypeCaller and Mutect2 (#7384)
  • Mutect2: the --genotype-germline-sites argument is no longer marked as experimental (#7533)

• GenotypeGVCFs / CombineGVCFs

  • Updated CombineGVCFs and GenotypeGVCFs to handle "reblocked" GVCFs with diploid data that are potentially missing hom-ref genotype PLs (#7223)
  • Homozygous reference genotypes with no PLs and zero depth are now output as no-calls by GenotypeGVCFs (#7471)
  • Bug fixes for GenotypeGVCFs/GnarlyGenotyper when allele-specific annotations have empty values due to lack of informative reads or no depth (#7491) (#7186)

• GenomicsDB

  • Added a new --call-genotypes GenomicsDB argument, enabling output of called genotypes (i.e. not ./.) when tools like CombineGVCFs and SelectVariants read from a GenomicsDB workspace (#7223)
  • Added a --bypass-feature-reader argument to GenomicsDBImport to allow the C-based htslib VCF reader implementation to be used instead of the Java implementation (#7393)
    • Using this option will reduce memory usage and potentially speed up the import process
  • Updated to GenomicsDB 1.4.2 (#7520)
    • This release fixes a commonly-encountered bookkeeping issue with GenomicsDB array fragments. Should fix errors of the type: "Error: Cannot read from buffer; Error: cannot load book-keeping" as reported in #7012
    • Full release notes are here: https://github.com/GenomicsDB/GenomicsDB/releases/tag/v1.4.2

• Funcotator

  • Fixed a StringIndexOutOfBoundsException in the protein change prediction code that could be triggered by certain indels. The fix avoids the crash by adding additional bounds checking. (#7513)
  • Allow FilterFuncotations to process multi-transcript genes (#7506)

• CNV Calling

  • CNV WDLs now handle BAM/CRAM index paths explicitly, as for cases where the index is not in the same path as its file (#7518)
  • gCNV in the CASE mode now fills in all hidden DenoisingModelConfig and CopyNumberCallingConfig arguments from the input model configuration (#7464)
  • Exposed number of samples used for estimating denoised copy ratios in gCNV via a new --num-samples-copy-ratio-approx argument (#7450)

• SV Calling

  • JointGermlineCNVSegmentation: bug fixes and refactoring (#7243)
    • A number of bugs, particularly with max-clique clustering, have been fixed, as well as a parameter swap bug in JointGermlineCNVSegmentation
    • Reworks classes used by JointGermlineCNVSegmentation for SV clustering and defragmentation. The design of SVClusterEngine has been overhauled to enable the implementation of CNVDefragmenter and BinnedCNVDefragmenter subclasses. Logic for producing representative records from a collection of clustered SVs has been separated into an SVCollapser class, which provides enhanced functionality for handling genotypes for SVs more generally.

• Notable Enhancements

  • Added a new Fragment Allele Depth (FAD) variant annotation (#7511)
    • This annotation is identical to the AD annotation except that allele support is considered per read pair, not per individual read

• Miscellaneous Changes

  • SplitIntervals: added new tool arguments to control output file naming (#7488)
  • Fixed an issue that caused the Travis CI test suite reports to fail to be uploaded (#7525)
  • Updated Travis CI authentication information (#7521)

• Documentation

  • Updated StrandBiasBySample documentation (#7283)
  • Updated MarkDuplicatesSpark documentation (#7191) (#7535)
  • Added a comment to ``.travis.yml` about the checkout depth (#7421)

• Dependencies

  • Updated to GenomicsDB 1.4.2 (#7520)
  • Updated sqlite-jdbc library to a newer version to support M1 Macs (#7519)