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illumina results to do genotype imputation,about AB to ATCG

Recently , I studied Illumina chicken 60k SNP chip. The orignal data was writed in plink map and ped file. My idea are as follows:

  1. use plink to QC
  2. convert the data after QC to vcf format
  3. use beagle4 to genotype imputation
  4. do some analysis

While in step 3, the beagle4 does not support for the AB format. I tried to use the gengen (refrence to http://gengen.openbioinformatics.org/en/latest/tutorial/coding/) to convert AB to ACTG. The gengen needs the snptable which has 4 columns like
Name SNP ILMN Strand Customer Strand
200003 [T/C] BOT TOP
200006 [A/G] TOP BOT
200047 [T/C] BOT TOP
200050 [C/G] TOP BOT
200052 [T/A] BOT TOP

I may got the first 3 columns but the last column data was gone. So here I want to ask you the way to got the data or the way to genotype impute without converting AB to ACTG . Look forward to your favourable reply.

snp illumina genotype imputation
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updated by mw955 • mw955 • written by sacuba1 • sacuba1

shoud i add a comment to up my post？

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written by sacuba1 • sacuba1

1 answer

Hey, I'm sure you've already figured this out but for anyone else reading this, check the documentation for gengen:

"one can easily generate such a file from the BeadStudio software: simply click the "SNPTable" tab after opening a project file, then use "column chooser" to select the "Name", "SNP", "ILMN Strand" and "Customer Strand" columns only, then click "export" to save the output to a file with the four columns."

http://gengen.openbioinformatics.org/en/latest/tutorial/coding/

Hope it helps someone, I spent the day building files for GenGen and made the mistake of skimming over the documentation. Could have saved me time if I read it the first time.

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written by mw955 • mw955

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