Question: How to get the average number of pairwise differences among populations?
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gravatar for remi.b.md
2.7 years ago by
remi.b.md60
remi.b.md60 wrote:

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?

statistics software genome • 1.3k views
ADD COMMENTlink modified 2.7 years ago by Brice Sarver2.6k • written 2.7 years ago by remi.b.md60
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gravatar for Brice Sarver
2.7 years ago by
Brice Sarver2.6k
United States
Brice Sarver2.6k wrote:

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.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Brice Sarver2.6k
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