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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RT @kasper_lage: Public service announcement: @gaddyg account is showing a pulse again. All interested in cancer, genetics & science should…
30 Apr 16
@embatty @BrockhurstLab @conTAMInatedsci @alanmcn1 Unfortunately some code flaws cause >20+ ploidy to be v. slow. On to-fix list.
28 Apr 16
Right! And +1M back at you on being more specific about *which* technology/platform. #ngsmustdie
27 Apr 16
@MrsLaviniaG Having a distinguishing term is indeed useful. Point is it should be a meaningful term. Next-gen is no longer meaningful.
27 Apr 16
@BenNMiles Phones still smart(er) whereas NGS is based on past state. Collision w/ screening is real; but context disambiguates?
27 Apr 16

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.@gatk_dev The genotype likelihood blog post is very nice. Thank you! via @bricesarver
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@gatk_dev thanks, will certainly have a look over WDL + Cromwell. Also like the memes on front page!
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