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.

Return to topComment on this article in the forum

Mon 17 Mar 2014

At a glance

Follow us on Twitter

GATK Dev Team


@joonomics As long as they can learn... Team includes mathematicians, physicists incl. astronomer, without prior knowledge of bio.
31 May 16
Join the #GATK dev team! We have job openings for a Data Scientist and an Associate Software Engineer
29 May 16
RT @BroadGenomics: Broad Genomics celebrates sequencing over 250k genomes and exomes #thatsawholelotofsequence #peoplepower #nooneelse http…
21 May 16
Notes on differences in #GATK 3.5 test results between Java 7 to 8
20 May 16
@kunalchandratre Answered
16 May 16

Our favorite tweets from others

The @dgmacarthur lab leaving as they came, rock stars of science in their stretch limo
14 May 16
Hey @BroadGenomics we just flew past 250,000 exomes + genomes. Good job everyone.
13 May 16
@gatk_dev Hey guys thanks for another fantastic workshop, hope you all had a good time in the pub. I’m now back the other side of the wall
14 Apr 16
@gatk_dev @notSoJunkDNA The cloud giveth, the cloud taketh
6 Apr 16
.@gatk_dev The genotype likelihood blog post is very nice. Thank you! via @bricesarver
23 Mar 16
See more of our favorite tweets...
Search blog by tag

ad appistry ashg benchmarks best-practices bug bug-fixed cancer catvariants challenge cloud cluster commandline commandlinegatk competition compute conferences cram cromwell denovo depthofcoverage diagnosetargets error fix forum gatk3 genotype genotype-refinement genotypegvcfs google gvcf haploid haplotypecaller hardware holiday hts htsjdk ibm java8 job job-offer jobs joint-discovery key license media meetings mendelianviolations multisample multithreading mutect mutect2 ngs nt outreach pairhmm paper parallelism patch performance phone-home picard pipeline plans ploidy polyploid poster presentations press printreads profile promote reference-model release release-notes rnaseq runtime saas search selectvariants sequencing service slides snow speed status sting support syntax talks team terminology third-party-tools topstory trivia troll tutorial unifiedgenotyper variantannotator variantrecalibrator version-highlights versions video vqsr wdl webinar workflow workshop