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ReduceReads parallelism

aihardinaihardin Member
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.

Best Answer

  • CarneiroCarneiro Charlestown, MAMember
    Accepted Answer

    Yes, you need to run non overlapping (farther than read length apart) intervals independently and merge the results together.

    -nt is incompatible with Read Walkers, unfortunately.

Answers

  • CarneiroCarneiro Charlestown, MAMember
    Accepted Answer

    Yes, you need to run non overlapping (farther than read length apart) intervals independently and merge the results together.

    -nt is incompatible with Read Walkers, unfortunately.

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