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Parallelizing Mutect

vyellapavyellapa Member
edited April 2013 in MuTect v1

Mutect seems to be using some of the GATK walkers. If that true, can I parallelize somatic variant calling using "-nt" or "-nct" options? The problem I run into is that, the cluster resources cap wall-time allocations to a maximum of 96 hours. On some occasions, for WGS, this is not sufficient.


  • kmdailykmdaily Member

    I was trying to use the "-nt" flag with disastrous results. It seems that the ordering of the data was messed up, and using it caused MuTect to hang. It also did not improve runtime. Thanks to David Hoover of the Biowulf support staff for helping me diagnose problems with this. Though, other GATK tools warn when parallelization is not supported.

  • kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭

    The recommended way of parallelizing MuTect is via Queue, which can run locally on a cluster. I'll take a look at why there isn't a better warning when the -nt flag is passed (or just figure out why it's broken and make -nt work!)

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