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
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
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