I am planing to impute about 3000 samples using impute2. These have been filtered by smartpca to be European descendant. Should I use 1000G samples as reference panel, or should I filter the 1000G data to only use CEU and TSI? (or are there such panel for download directly)?
Another question. Given the size of my sample, should I do 1 step imputation, or 2 step? Thanks.