broadinstitute/gatk 4.2.5.0

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Download release: gatk-4.2.5.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/

Highlights of the 4.2.5.0 release:

• Fixed a GenotypeGVCFs IllegalStateException error reported by multiple users in #7639

• Added a new tool SVCluster that clusters structural variants based on coordinates, event type, and supporting algorithms.

Full list of changes:

• Joint Calling (GenotypeGVCFs / GenomicsDB)

  • Fixed an IllegalStateException in GenotypeGVCFs arising from GenomicsDB output with too many alts and no likelihoods, and also added a --genomicsdb-max-alternate-alleles argument that is separate from the --max-alternate-alleles argument used by GenotypeGVCFs (#7655)
    • This fixes the GenotypeGVCFs error reported in #7639
    • The new --genomicsdb-max-alternate-alleles argument is required to be at least one greater than the --max-alternate-alleles argument, to account for the NON_REF allele.
  • ReblockGVCF: fixed an edge case where hom-ref "variant" records with no data had wrong-sized PLs and didn't merge with adjacent blocks (#7644)

• SV Calling

  • Added a new tool SVCluster that clusters structural variants based on coordinates, event type, and supporting algorithms. (#7541)
    • Primary use cases include:
      • Clustering SVs produced by multiple callers, based on interval overlap, breakpoint proximity, and sample overlap.
      • Merging multiple SV VCFs with disjoint sets of samples and/or variants.
      • Defragmentation of copy number variants produced with depth-based callers.

• Mutect2

  • The palindrome ITR artifact transformer now skips reads whose contigs are not in sequence dictionary (#6968)
    • This fixes a NullPointerException error in Mutect2 reported in #6851

• GATK Engine

  • Added a new read filter, ExcessiveEndClippedReadFilter (#7638)
    • This filter will keep reads that have fewer than the specified number of clipped bases on either end.
    • Designed with long reads in mind, and as a result has a default value of 1000.