Release notes for GATK version 3.1

Mon 17 Mar 2014

GATK 3.1 was released on March 18, 2014. Highlights are listed below. Read the detailed version history overview here:

Haplotype Caller

  • Added new capabilities to the Haplotype Caller to use hardware-based optimizations. Can be enabled with --pair_hmm_implementation VECTOR_LOGLESS_CACHING. Please see the 3.1 Version Highlights for more details about expected speed ups and some background on the collaboration that made these possible.
  • Fixed bugs in computing the weights of edges in the assembly graph. This was causing bad genotypes to be output when running the Haplotype Caller over multiple samples simultaneously (as opposed to creating gVCFs in the new recommended pipeline, which was working as expected).

Variant Recalibrator

  • Fixed issue where output could be non-deterministic with very large data sets.


  • Fixed several bugs where bad input were causing the tool to crash instead of gracefully exiting with an error message.


  • RandomlySplitVariants can now output splits comprised of more than 2 output files.
  • FastaAlternateReferenceMaker can now output heterozygous sites using IUPAC ambiguity encoding.
  • Picard, Tribble, and Variant jars updated to version 1.109.1722.

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Mon 17 Mar 2014
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GATK Dev Team


@BrandonL_Pierce Added to
10 Oct 15
@ZaminIqbal Different number of reads? Could be downsampling settings, visibility of duplicates, or other filters. See alignment prefs.
10 Oct 15
@dklevebring @fiamh Yep it's a pain -- we're working on some functionality to handle this better.
9 Oct 15
RT @WileyGenetics: #ASHG15 Tomorrow morning's #GATK has sold out! But don't fret! You can still learn how to use #GATK here:…
8 Oct 15
RT @dgmacarthur: AH: we'll shortly be rolling out an ExAC update that flags phase-dependent variants; GATK now automatically outputs phase …
8 Oct 15