SNPgenie for one bacterial strain

[SolayMane]

Dear Chase,
I have a vcf file for snps of one strain against a ref. Can I use SNPgenie to calculate Pi trough the whole genome using sliding window?
Sincerely

[singing-scientist]

Greetings @SolayMane ! Yes you can. If you want to do it yourself for a certain window, πN can be calculated as sum(N_diffs) / sum(N_sites), where N=nonsynonymous, and πS in the same way using S (for synonymous). But make sure the windows are not too small, or they will be subject to wild random fluctuations! Let me know if that helps.