[adegenet-forum] Retrieving population allele frequencies of SNPs using HGDP file

Davide Piffer pifferdavide at gmail.com
Wed Oct 4 15:08:38 CEST 2017


I am new to Adegenet. I would like to retrieve population frequencies of
SNPs (using rsID) from the HGDP file "HGDP_FinalReport_Forward.txt" :

However, the file lacks population information. It contains SNPs x
I need a file structured like the eHGDP (except with SNPs and not
microsatellite data) file provided with the package, that can be easily
converted into genpop file and then compute the frequencies via makefreq.
Do you know if there is any such file downloadable on the internet?
i guess there must be a way to produce such a file using ADEGENET starting
from raw data. but my knowledge of this package is not advanced enough yet.

Best wishes,

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