Question: Converting numeric to alphanumeric allele codes
0
gravatar for emyli
16 months ago by
emyli0
emyli0 wrote:

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.

ADD COMMENTlink modified 16 months ago by tarek.mohamed230 • written 16 months ago by emyli0
1
gravatar for tarek.mohamed
16 months ago by
tarek.mohamed230
tarek.mohamed230 wrote:

Hi,

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

Tarek

ADD COMMENTlink written 16 months ago by tarek.mohamed230

Works perfectly, thank you!

ADD REPLYlink written 16 months ago by emyli0
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