I have a list of SNPs of the type rs17004888. I want to extract the corresponding SNPs from binary plink files and generate a .raw subset of the binary file.
When I ran the command
plink --bfile (path to binary) --extract (path to SNP list) --recodeA --out (output name)
I get the following:
0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 0 SNPs
I suspect that the SNP names in the binary file are of the type
rs17004888_A, and thus it cannot find any matches.
How can I deal with that?