Release notes for GATK version 3.1

Mon 17 Mar 2014
Share

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 top

Mon 17 Mar 2014
Share
Comment on this article in the forum


Search blog by tag

2013 ad agbt14 appistry baserecalibrator belgium best-practices blog bqsr broken-links brussels bug bug-fixed cancer catvariants challenge combinegvcfs combinevariants commercial community compbio competition conferences depthofcoverage diagnosetargets documentation downtime error fastaalternatereferencemaker forum gatk gatk-3-0 gatk-3-1 gatk-3-2 gatk-lite gatk2 gatk3 genotypegvcfs gsa gsa-announce gvcf haplotypecaller hardware holiday indelrealigner intel job job-offer jobs joint-analysis joint-discovery key license lite media meetings multisample multithreading mutect nt optimization pairhmm paper performance phone-home pipeline poster presentations press printreads queue randomlysplitvariants readbackedphasing reducereads reference-model release release-notes rnaseq scatter-gather selectvariants slides spam splitncigarreads support talks topstory trivia tutorials unifiedgenotyper userstories validatevariants variantannotator varianteval variantrecalibrator variantstobinaryped version-highlights video videos webinar workshop


GATK Dev Team

@gatk_dev

RT @edgenome: Today's attendees at our 'Linux for Genomics' workshop. Keep tuned for more info on forthcoming courses and events... http://…
25 Jul 14
RT @TheAllium: Broad Institute “Can’t be bothered anymore” with donations below $200 Million http://t.co/KOLby8OlXA via @theallium
24 Jul 14
RT @appistry: Join us tomorrow for our #webinar discussing the #PickMyPipeline Challenge! #NGS http://t.co/iK4s52xpzf
23 Jul 14
New Pipeline Challenge from @Appistry http://t.co/m9jWWmRn9g
23 Jul 14
@Elfsevier @jermdemo Isn't bro-ness itself a disease? Or do you mean diseases that are comorbid to bro-ness?
22 Jul 14