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ReduceReads parallelism

aihardinaihardin Member Posts: 3
edited August 2012 in Ask the GATK team

I'm working with ReduceReads and would like to use it in some kind of parallel mode. The presentation mentions that a 50x way run may drastically reduce run time but I'm not sure how to invoke this. I tried -nt and it complained. Should I be giving it multiple intervals and merging? If so, how does it deal with edge variants?

Thanks.

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