How to get the average number of pairwise differences among populations?
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?
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Brice Sarver
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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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