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  • splitting haplotyepecaller onto multiple threads

    Hi all,

    Quick question, I am doing some whole genome and am using the GATK haplotypecaller. To speed things up, I would like to break the genome into smaller chuncks and run each chromosome separately on its own thread (using -L options with a bed file for each chromosome). This will produce multiple gvcf files for 1 sample. If I use the genotypeGVCFs function, will it treat the gvcf's with the same sample name as a single file? Would the combineGVCFs do the same thing and that should be done first?

    Thanks

  • #2
    If you're just going to split things to run on individual threads, then why not just use the -nt option? What you suggest would only make sense if you're using a cluster and want to split individual samples across nodes.

    Comment


    • #3
      Sorry, I wasn't clear, but I am going to be splitting the samples across nodes on a cluster. also on the GATK documentation page, there is a caveat listed:

      Many users have reported issues running HaplotypeCaller with the -nct argument, so we recommend using Queue to parallelize HaplotypeCaller instead of multithreading
      I assume that means that the -nt options shouldn't be used, otherwise it would be a better way to do things.

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      • #4
        Ah, guess I've just never run into issues with it.

        Comment

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