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convert PLINK file to genepop

Hello, I was wondering if anyone knows how to convert a PLINK file (.ped or .bed) to genepop.

I have PGD spider but it doesn't use population information so the output file is only one pop.

I stratified allele frequecies frequencies (.frq) but this file doesn't work in PGD.

Any ideas?

Thanks!

snp genome snp
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updated by Noeliton • Noeliton • written by age00 • age00

1 answer

PGDSpider performs the conversion as long as the Plink (.ped) file contains columns with information about family, sample ID, sex, phenotype, etc. Missing data can be represented by zero (0). This information must be marked as missing or not in the PGDSpider conversion options, and the file generated in GenePop format will display the correctly separated populations.

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written by Noeliton • Noeliton

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