We're very excited to announce that we have started collaborating with a team from Intel (yep, that Intel) to optimize key parts of the GATK code to make it run faster. The first fruits of this collaboration --a set of hardware-based optimizations for the PairHMM algorithm in HaplotypeCaller-- are available as of today in version 3.1 of the GATK. Please see the release notes and version highlights in the Version History section of the Guide for details.

Of course this is only the beginning, and we're looking forward to delivering more performance improvements for various other GATK tools moving forward as part of this collaboration.

What's really cool is that this collaboration extends beyond our little GATK team; the Intel Bio Team is also going to be working with other groups at the Broad Institute to make their software run faster as well, all with the goal of accelerating scientific research and discovery.

For more details and background information, see the Bio-IT World story here: http://www.bio-itworld.com/2014/3/20/broad-intel-announce-speed-improvements-gatk-powered-by-intel-optimizations.html

Comment on this article in the forum

At a glance

Follow us on Twitter

GATK Dev Team


@vibbioinfocore Thanks for having us over! Great group of participants, lots of good questions!
25 Feb 17
Slides, tutorial materials from #GATK workshop in Leuven, Belgium posted at https://t.co/LaXzONIp1C
19 Feb 17
RT @EMBL_ABR: Register your interest now in training in @gatk_dev @BroadGenomics https://t.co/gwEzuwOZYP to be run in Aus by @BioplatformsA…
19 Feb 17
#GATK Support team appreciation day -- say hi and get a prize! https://t.co/J71I4FL9zA
23 Jan 17
RT @EricTopol: Great explainer of human genome structural variation https://t.co/BaAWWmi30A @broadinstitute https://t.co/282chNv4oI
21 Jan 17

Our favorite tweets from others

Our 3-day course on GATK https://t.co/mtN60KRTyS finished - 38 participants very happy! Big thanks to @gatk_dev team for excellent lessons.
24 Feb 17
@froggleston @dgmacarthur Sounds like ExAC is reaching Uber stage. ‘Uber but for pizza’. ‘ExAC but for wheat’.
14 Jan 17
#ESRenpeinture grad school - postdoc - after postdoc https://t.co/o3vQMgBDgk
6 Jan 17
Really happy to have you again this year! @VIBLifeSciences https://t.co/8rg5VQ2fbX
3 Jan 17
Currently in a time-out for saying that duck fat had a certain "je ne sais quack" at the thanksgiving dinner table.
25 Nov 16
See more of our favorite tweets...
Search blog by tag

appistry ashg ashg16 benchmarks best-practices bug bug-fixed cancer cloud cluster cnv collaboration commandline community compute conferences cram cromwell depthofcoverage diagnosetargets error forum gatk3 gatk4 genotype-refinement genotypegvcfs google grch38 gvcf haploid haplotypecaller hg38 holiday hts htsjdk ibm intel java8 job job-offer jobs license meetings mutect mutect2 ngs outreach pairhmm parallelism patch performance picard pipeline plans ploidy polyploid poster presentations printreads profile promote release release-notes rnaseq runtime saas script sequencing service slides snow speed status support syntax talks team terminology topstory troll tutorial unifiedgenotyper vcf-gz version-highlights versions vqsr wdl webinar workflow workshop xhmm