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

[Lisamjb]

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!

[Dameon]

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.