software to caculate gene frequency based on SNP ped and map file

Question

[xiaojuhu13]

I had SNP-genotype (Illumina SNP-chip) data (ped and map files). Now I'd like to construct phylogeny tree with bootstrap support based on total 46 populations. I used the Phylip for the analysis, but how to use the ped and map files to calculate gene frequency as input for the Gendist for the population genetic distance?

Answer 1

[LChart]

You can use plink --freq in conjunction with --keep to compute frequencies per-population. It will need to be re-formatted into the Gendist input, but there's not much more to do than paste