Converting numeric to alphanumeric allele codes
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4.2 years ago
emyli ▴ 10

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.

genomestudio allelecodes pedfile • 1.2k views
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4.2 years ago
tarek.mohamed ▴ 310

Hi,

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

Tarek

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Works perfectly, thank you!

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