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Old 10-02-2015, 05:43 AM   #2
WhatsOEver
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Location: Germany

Join Date: Apr 2012
Posts: 215
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I have no experience with SNP chip data no can I suggest an existing program that is able to this, but from your description it seems to be a rather simple lookup problem for which some self-coding should be sufficient.

What you need to do is reading linewise through your file:
AX-51 2 1 2 1 1 2 1 2 1 2 2 1 1 2 0 2 2 2 0 1 0 2 2 1 2 2 -1 2
.

For each line you take the SNP_ID in the beginning and look for its corresponding genotype in the map file (for AX-51 you may get refGeno = A / altGeno=G)

Afterwards you simply go through the fields of the prediction and replace the numbers with the genotypes (e.g. if "0" then refGeno, elif "2" then altGeno, ...)

If you have no programming experience, you might even use excel/open office (vlookup) for this. Certainly not the best way to do, but still possible
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