I am trying to use PRSice. Unfortunately, my target sample has fewer SNPs than my discovery/base sample, as it comes from different platforms. My question is of a methodological nature: I could of course impute the missing SNPs, and PRSice explicitely mentions it can handle such information. However, PRSice also performs clumping. If I'm not mistaken, imputation fills in missing SNPs using linkage disequilibrium information, while clumping then tries to estimate LD and reduce the SNPs to an independent set. Wouldn't imputation and clumping pretty much cancel out then? I'm not sure what the best practice is in this situation.
PRSice has its google group for quick answers https://groups.google.com/forum/#!forum/prsice