I have a list of SNPs for which I want to prune to a smaller set. I used to prune through PLINK, however, now the genotype I have for each SNP is no longer AA,AT,TT like that kind. But instead, the genotypes can take any numerical value between 0 and 2, like 1.9986 since they are imputed values.
Can someone offer me some advice on how to deal with this situation? Thank you very much!