GATK 3.1 was released on March 18, 2014. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history


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.

CalculateGenotypePosteriors

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

Miscellaneous

  • 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

@gatk_dev

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 https://t.co/440d1Kybte
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

Our favorite tweets from others

@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! https://t.co/ZFPiZVaoKe via @bricesarver
23 Mar 16
@gatk_dev thanks, will certainly have a look over WDL + Cromwell. Also like the memes on front page!
18 Mar 16
Great to learn about GATK at the GATK workshop at @UCLA. Thanks @gatk_dev team!
2 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 combinegvcfs commandline commandlinegatk competition compute conferences cram cromwell denovo depthofcoverage diagnosetargets error fastaalternatereferencemaker fix forum gatk3 genotype genotype-refinement genotypegvcfs google gvcf haploid haplotypecaller hardware holiday hts htsjdk ibm job job-offer jobs joint-analysis 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 randomlysplitvariants readbackedphasing reducereads reference-model release release-notes rnaseq runtime saas search selectvariants sequencing service slides snow speed splitncigarreads 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