I'm working with a GWAS dataset and I am not so experienced yet with imputation of missing genotypes. But I managed to phase my dataset with SHAPEIT, impute with IMPUTE2 and did an association analysis with SNPTEST, so far so good. But: how do I now adjust for population stratification? I don't find any option in SNPTEST to adjust for Genomic Control, so I guess it can be done by adjusting for principal components as covariates. But how do I calculate principal components from IMPUTE2 output (file types: .gen; .gen_info)??
Thanks a lot! Frank