GATK 3.8 was released on July 28, 2017. Itemized changes are listed below. For more information on what you should care about, see the user-friendly version highlights.

Performance improvements / accelerations

  • Add the Intel GKL as a dependency, and turn on the Intel inflater/deflater by default
  • Use GKL's implementation of Vector Logless Pair HMM (HaplotypeCaller and MuTect2)
  • Add FPGA support for PairHMM via GKL (experimental)

Notable tool behavior change

  • In VariantsToTable, flip handling of missing annotation values: allow by default (print NA for null object), deprecate --allowMissingData, add --errorIfMissingData flag

Improvements to germline calling toolchain

  • Change calculation of rank sum to be the median of the per-sample rank sums (because the rank sum across all sample data did worse for biallelics)
  • Improve VQSR model serialization functionality and allow serialized model reports to be read into the variant recalibrator to recreate a GMM from a previous VQSR run
  • Allow disabling of BadMateFilter in HaplotypeCaller

Bug fixes

  • Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref
  • Fix ClippingOP.getNewAlignmentStartOffset() to handle N cases properly
  • Fix FindCoveredIntervals so -minBQ, -minMQ and -cov work as expected
  • Fix thread safety bugs (upstreamDeletionsLoc and practicalAlleleCountForPloidy)
  • Fix bug in depth of coverage for partitioning by library
  • In GenotypeGVCFs, total ploidy does not have to equal the number of priors
  • Explicitly report AD and DP as zero if there is no read coverage
  • GenotypeGVCFs and CombineGVCFs now throw errors when AS annotations are not present if allele-specific mode is activated
  • Copy Program Records (PG) from input BAM to -bamout file (failure to do so caused some validation failures)

Docs / logging

  • Assorted corrections and improvements in documentation, error messages and logging rules
  • Archive GATK3-specific docs from the forum

Misc engine

  • Bump htsjdk to ver 2.10.1 and Picard to ver 2.10.2

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