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Old 02-01-2012, 12:02 AM   #1
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Location: Melbourne

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Default Synonymous vs. non-synonymous mutations in pileup data

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 at 12:22 AM.
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Old 02-01-2012, 12:57 PM   #2
Location: St. Louis, MO - USA

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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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