Converting numeric to alphanumeric allele codes

Question

[emyli]

I have a .ped file generated using SNP chip .idat data processed using the GenomeStudio GT module. The genotypes are coded using allele values of 1, 2 , 3 or 4. Is there a away to convert these to the base call ie. A, C, G or T? I assume each number corresponds to a base call, but am unsure of how they match up.

Answer 1

[tarek.mohamed]

Hi,

You can use --alleleACGT with --recode in plink.

Tarek

[emyli]

Works perfectly, thank you!