4.0.6.0

Highlights of this release include:

• A new version of GenomicsDB that brings many long-requested features such as support for multiple intervals in GenomicsDBImport
• A significantly (~33%) smaller GATK docker image
• An important bug fix for the -new-qual option in GenotypeGVCFs/HaplotypeCaller/Mutect2

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:

• GenomicsDB: new version with many long-awaited features and bug fixes (#4645)

  • Multi-interval support in GenomicsDBImport (#3269)
    • Now you can specify multiple -L intervals when importing variants into GenomicsDB using GenomicsDBImport, instead of having to specify one interval per invocation.
  • New protobuf-based API to allow configuration without editing JSON files
  • Support for sites-only queries
  • Support for returning the genotype (GT) field in queries
  • Fixed bug where records with spanning deletion alleles could cause reads from GenomicsDB to fail (#4716)

• Reduced the size of the GATK docker image by approximately 33%, from ~5.3 GB to ~3.5 GB (#4955)

• Fixed a regression in the -new-qual option for GenotypeGVCFs/HaplotypeCaller/Mutect2 that was introduced in GATK 4.0.5.0 (#4980)

  • There was a precision issue in the AlleleFrequencyCalculator when running with -new-qual that could cause a crash at certain sites (specifically, sites with spanning deletions and highly unlikely alt alleles).

• HaplotypeCaller: don't count qual = 0 sites as polymorphic for GVCF mode (#4967)

• ValidateBasicSomaticShortMutations: added a new optional argument to produce summary table output (#4982)

• ExtractOriginalAlignmentRecordsByNameSpark: added a new optional argument to invert the logic in the read-name filtering (#4944)

• Separated out the "variant calling" integration tests from the rest of the integration tests to speed up overall test suite runtime in travis (#4984)