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


@ewanbirney We'll be in touch re: beer/choc, need to consult the full team after the holiday. Thanks :)
27 Nov 15
@akiezun Brace yourselves, the beer is coming! @ewanbirney @chapmanb
25 Nov 15
@micknudsen Hmmmm no, not even close :D
25 Nov 15
@micknudsen Oh, you have a 10-week old baby too? ;)
25 Nov 15
Oh wait, @micknudsen got there first. You guys are fast! I'm calling timezone shenanigans.
25 Nov 15