Folded vs. unfolded SFS for population genetic summary statistics

[Joshua Penalba]

Hi,

I just wanted to clarify some assumptions for both the single and multipopulation population genetic statistics (Watterson's theta, pi, Tajima's D, Fst, segregating sites). I'm hoping that I didn't miss this in the manual. I'm currently inputting a folded SFS from ANGSD into dadi to do my analyses. Does the calculation for these measures assume an unfolded SFS? If so, since I don't have an outgroup to properly polarize my SNPs, would there be a "good practice" alternative? Thanks in advance for the response. 

Best,

Josh

[Gutenkunst, Ryan N - (rgutenk)]

Hello Josh,

The number of segregating sites doesn’t depend on whether the data are folded, so that’s okay. Watterson’s theta only depends on the number of segregating sites, so it’s okay too. Calculation of pi depends on frequency x times (1-x), which is symmetric with respect to folding, so it should be okay. Tajima’s D depends only on the other quantities, so it’s also okay. It’s less obvious for Fst, but that also doesn’t depend on folding.

Best,

Ryan

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Ryan Gutenkunst
Assistant Professor of Molecular and Cellular Biology, University of Arizona
phone: (520) 626-0569, office: LSS 325, web: http://gutengroup.mcb.arizona.edu

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[Joshua Penalba]

Fantastic! That's a relief to hear. Thanks Ryan!