this is a very basic question, but I cannot find it explicitly stated anywhere: When exactly should I filter the info scores after imputation?
I did imputation in Impute2 and am planning on using SNPtest to analyze, but cannot tell if I should filter the scores in Impute2, SNPtest, Gtool, QCtool, or through python.
I'm hoping to get rid of the poorly imputed results (with an info score cutoff <0.5) in a population of ~4000 (half cases, half controls). After this, I'm running an association analysis -- probably through PLINK, but I'm still figuring out the best way to go from Impute2 to PLINK.
Any help would be greatly appreciated!!