Genotypes conversion (SNP chip)

[clarissaboschi]

Hi all,
I have a big input file from 28 individuals which were genotyped by 600 K SNP chip (Affymetrix). I have about ~500,000 genotypes for each individual.
But my file has a particular format for the genotypes, which is:

-1= no call
0=AA (homozygous for the reference allele)
1=AB
2=BB (homozygous for the alternative allele)

My file is:
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
AX-58 2 2 2 2 2 1 1 2 1 2 1 2 2 2 1 2 2 2 2 2 2 2 2 1 2 2 2 2

I have another file with the alleles information and position (map file):
SNP_ID Chr Pos Alele_A/Alele_B
AX-751 1 306 T/C
AX-758 1 727 A/G

I need to convert the file 1 with their respectives alleles. I tried to use Plink, but I was not able to convert the file.

Any suggestion??

thanks
Clarissa

[WhatsOEver]

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