Post date: Nov 14, 2019 4:34:55 PM
This post was moved from a different page, hence it is out of order and should be the first post on this page.
This is the frog hybrid zone project I am working on with Maria. She sent me variant data in gl format. My first step was to split this by population and estimate allele frequencies. The data (192 individuals, 103,825 SNPs) are in variants.gl in /uufs/chpc.utah.edu/common/home/u6000989/projects/frogs/variants/. The individual gl files I generated are for each of 15 populations and begin with frogs*.
I used estpEM to generate allele frequency estimates (tolerance 0.001, number of iterations = 20). The output files are p_frogs* or p_variants.txt. I moved these to an freqs sub-directory.