How to get the average number of pairwise differences among populations?
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4.8 years ago
remi.b.md ▴ 60

I have genetic data in .structure and .vcf format (and can easily reach other formats with PGDSpider). The population of interest is structured and I would like to calculate the average number of pairwise differences (over a given window) between any pair of populations.

Is there an existing tool that would do the job for me?

genome statistics software • 2.0k views
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Entering edit mode
4.8 years ago
Brice Sarver ★ 3.6k

One way: pid() in R. Multiply by sequence length. Average over all individuals by applying over a matrix.

Edit: this is probably too complex for what you want to do. Try ngsDist.

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