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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@iskander @NJL_NGS Treat them like any other read, no special handling. Problems arise in CIGAR functions that don’t know how to handle Ns.
7 Dec 16
@iskander @NJL_NGS By default we error out. Possible to override using -U ALLOW_N_CIGAR_READS but tool may crash. Is unsupported usage.
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RT @geoffjentry: How @WDL_dev empowers a biochemist w/o programming background to perform large scale genomics analyses: https://t.co/BxAnK
6 Dec 16
@iskander @NJL_NGS Not aware of any, sorry.
5 Dec 16
@NJL_NGS @iskander No, GATK tools don't handle Ns in CIGAR, splitting is obligatory. See RNAseq guidelines in docs for more details.
5 Dec 16

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