denominators for pi_s and pi_4fold

[OBBARD Darren]

Hi all!

We are reinventing wheels again, and I thought I'd survey Ashworth for current (best or just Ashworth) practice when calculating genetic diversity summary stats from genome-scale data:

pi_a
pi_s
pi_0fold
pi_4fold

What are the standard packages for doing this from a vcf?

With SnpEff its easy to sort a vcf into syn and non-syn variants, but what is everyone's preferred way (say from a gtf and fasta genome) of obtaining the denominator? Or of directly calculating pi_0fold and pi_4fold?

Or does everyone have their own wheels?

Thanks!

D


--
Darren Obbard
darren...@ed.ac.uk

Institute of Evolutionary Biology
University of Edinburgh
Room 2.09, Ashworth 2, Charlotte Auerbach Road
Edinburgh EH9 3FL

Office 0131 651 7781
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http://obbard.bio.ed.ac.uk/
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