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  • Lisamjb
    Junior Member
    • Feb 2012
    • 1
    #1

    Calculation of pi(a)/pi(s) for sequence data in pileup format

    Hi!
    Does anyone know of any program that can identify synonymous and non-synonymous mutations for population data in pileup format? I'm particularly interested in calculating pi(a)/pi(s). SAM format is also okay too, but I need something that can deal with Ns.
    Thanks in advance for your help!
    Last edited by Lisamjb; 02-01-2012, 01:22 AM.
    Tags: None
    • Dameon
      Member
      • Dec 2011
      • 14
      #2
      snpEff will identify synonymous and non-synonymous mutations for SNP data in pileup format. I am not sure how it will perform with population data though.

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