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


@TechnicalVault @emblebi Indeed, will be credited clearly in the release notes -- pls forgive @akiezun's enthusiasm over CRAM in #GATK ;)
19 Nov 15
@GuidoLeoni1 We had some glitches today, will look into it with Vanilla Forums tech support.
19 Nov 15
RT @akiezun: When it comes out, GATK 3.5 will work on CRAM files. Just a few days out. Coming to you from @gatk_dev
19 Nov 15
@isugif @sciencegurlz0 FYI we have some docs on using #GATK for RNAseq here
18 Nov 15
@K_G_Andersen Um. Ok. If you tell us what's wrong we'll try to help fix it...
18 Nov 15