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


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New #GATK web address: https://t.co/SmXppw36ir (but www links or bookmarks will still work) https://t.co/PqbYbGhSWH
20 Jul 16
@yokofakun GenomeSTRiP is developed by a different group (Bob Handsaker at Harvard); expect Bob to answer on the forum.
18 Jul 16
@TechnicalVault and we're currently working on a public roadmap document for GATK4 (2/2)
11 Jul 16
@TechnicalVault Happy to discuss roadmap, not meant to be secret. We try to post updates on blog, eg https://t.co/1xKZXf3dLu (1/2)
11 Jul 16
@biobenkj @torstenseemann @broadinstitute Post question to #GATK forum -> will be answered. https://t.co/bEGBZUtyjL
11 Jul 16

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You’re right @gatk_dev honesty is key! About variants manual filtering: “In any case you're probably in for a world of pain.” Ha now I know!
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There is no NGS, NG is today so should only be called high-throughput sequencing #CSC #GATKworkshop https://t.co/paHcNimD7o
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The @dgmacarthur lab leaving as they came, rock stars of science in their stretch limo https://t.co/IQ0eCOT5H6
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13 May 16
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