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


- Recent posts


- Upcoming events

See Events calendar for full list and dates


- Recent events

See Events calendar for full list and dates



- Follow us on Twitter

GATK Dev Team

@gatk_dev

Some really great points here. We teach multiple workshops every year; while the short format is not the best possi… https://t.co/r2EoyKNBFK
14 Dec 17
@nickschurch @pathogenomenick @nanopore Heeey... well you may have a point. We don't really do dirty ;) Never tried… https://t.co/zTH5QI89XZ
14 Dec 17
What's new in GATK4? In this short video, Laura Gauthier explains how the speed and scalability of joint calling is… https://t.co/EAPdrZcqJI
14 Dec 17
What is truth? Or, how an accident of nature can illuminate our path https://t.co/qperntHUVz
8 Dec 17
Why is HaplotypeCaller slower in the most recent GATK4 beta versions? Because it's saving its strength for the 4.0… https://t.co/p3ZBPojxkR
6 Dec 17

- Our favorite tweets from others

My first @gatk_dev blog-post https://t.co/JwVzAtqDvt about the CHM cell-lines experiment we now use as benchmark da… https://t.co/8VdqG6H4Zk
9 Dec 17
Wanna be a baller, HaplotypeCaller 20K genotypes in the VCF file Caller, gettin' phased tonight https://t.co/bOGSI4UL23
17 Nov 17
This amazing genomics toolkit helps researchers find insights that save lives - I know! GATK users - please provide… https://t.co/gdY4FDPX8K
2 Nov 17
using GATK to identify SNPs while handing out candy... Happy Halloween! @broadinstitute @gatk_dev #bioinformatics #researchisfun #Halloween
31 Oct 17
Although it made me cry sometimes, I owe them a lot and love them much more. https://t.co/vUj0cBllgn
16 Oct 17
See more of our favorite tweets...