View Single Post
Old 09-30-2015, 10:46 AM   #1
clarissaboschi
Member
 
Location: US

Join Date: Apr 2010
Posts: 63
Default Genotypes conversion (SNP chip)

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
clarissaboschi is offline   Reply With Quote