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  • GATK UnifiedGenotyper pooled sample

    Hi!

    How do I use UnifiedGenotyper in pooled samples ?

    I have a bam file in which there are 5 individuals for each pool.

    do GATK UnifiedGenotyper take into account of pooled sample ?

    thank you!
    Last edited by sirmark; 03-11-2013, 03:16 PM.

  • #2
    ok, I have corrected the request, that before was too specific

    Comment


    • #3
      As long as the sample names are different in the BAM header, it should be fine.

      Comment


      • #4
        --sample_ploidy 5 is the option to use ?

        Comment


        • #5
          Just as a general recommendation/warning: if your 50 haploid genomes are truly pooled and then sequenced then the -ploidy 50 is correct. But if your samples are individually barcoded (or sequenced separately) and hence are marked as separate samples in your BAM then that would be incorrect: you should set -ploidy 1 and you'll get in your output your individual genotypes for each sample. - See more at: http://gatkforums.broadinstitute.org....Jkr7fN80.dpuf
          Got this off the GATK forum.

          I assumed your data was from different individuals in one bam.
          Last edited by vivek_; 03-12-2013, 01:32 PM.

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          • #6
            ok, thank you!

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