Release notes for GATK version 3.8

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited July 2017 in Announcements

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
Post edited by Geraldine_VdAuwera on
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