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

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?

snp genotype
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updated by LChart LChart • written by xiaojuhu13 xiaojuhu13

1 answer

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

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written by LChart LChart

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