I want to exstract a single SNP from my .impute file (created using IMPUTE2). I want this information as a plink file with genotype on all in individuals in the study at this particular posistion. When working with non-imputed data I've used this command line:
./plink --bfile GWASfile --snps rsXX --make-bed --out outputfile
This does however not work when I dont have the file in a plink format, but in a large .impute file.
Does anyone know how I can make this plink file from the impute file?