Broad collaboration with Intel Bio Team

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:

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GATK Dev Team


#GATK poster is online at for anyone who missed it at #ASHG15
8 Oct 15
Bring on the 20,000 WGS! Great test of the #GATK's GVCF workflow at the next order of scale since ExAC
8 Oct 15
@WileyGenetics No worries, thx for trying to boost the paper's visibility. But our software made an evolutionary jump in the meantime.
8 Oct 15
Looking fwd to the party :)
8 Oct 15
@WileyGenetics Paper is already outdated, so plz use #ASHG15 workshop materials that we'll post on our website to learn the latest version
7 Oct 15