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  • Exome data: how to filter by cases and controls?

    Hi all,

    I'm currently trying to figure out how to sort the exome data from several samples so that I would have a list with SNPs/indels including the SNPs/Indels shared by all of the patients and none of the controls.

    i.e. I would like to filter out all of the SNPs/indels from the controls and find a common mutation in the cases.

    Does anyone know some nice program that could do this? I tried to use exome-assistant, but it seems to accept only data in hg18 format... My data is hg19.

    Sincerely,
    Sini

  • #2
    I think BEDtools should be able to do this...
    For instance, you can merge the SNPs/INDELs(using mergeBed), use multiInteresectBed for getting SNPs/INDELs common to all cases, then use subtractBed to get case specific variants.

    Comment


    • #3
      Thank you ersgupta! I'll look into BEDtools

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