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

Question

[remi.b.md]

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?

Answer 1

[Brice Sarver]

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.