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 acceleration ad agbt14 appistry ashg ashg2014 belgium best-practices beta blog brussels bug bug-fixed cancer catvariants challenge cloud combinegvcfs combinevariants commandline commandlinegatk commercial compbio competition conferences denovo depthofcoverage diagnosetargets downtime error fastaalternatereferencemaker fix forum gatk gatk-3-0 gatk-3-2 gatk3 genotype genotypegvcfs genotyperefinement google gsa gvcf haploid haplotypecaller hardware holiday htsjdk ibm indelrealigner job job-offer jobs joint-analysis joint-discovery key license media meetings mendelianviolations multisample multithreading mutect nt pairhmm paper patch performance phone-home picard pipeline ploidy polyploid poster presentations press printreads queue randomlysplitvariants readbackedphasing reducereads reference-model release release-notes rnaseq search selectvariants service slides snow spam speed splitncigarreads status sting support syntax talks team third-party-tools topstory trivia troll unifiedgenotyper variantannotator variantrecalibrator variantstobinaryped version-highlights versions video videos vqsr webinar workshop


GATK Dev Team

@gatk_dev

https://t.co/RdoGBtkeuA
30 Jul 15
RT @fdmts: Compression, deduplication, and caching perform radically better on files made exclusively of zeroes. #protip #bestpractice #ben…
29 Jul 15
RT @dgmacarthur: Interested in using massive data sets to improve the lives of rare disease families? Work with my team: http://t.co/eGhYot…
29 Jul 15
RT @fdmts: @gatk_dev uses CRISPR to merge collisions in the code repository. #crisprfacts
23 Jul 15
New patch version 3.4-46 released; get the latest #GATK bugfixes now now https://t.co/m8nc3RvoWA
9 Jul 15