Ambiguous SNPs

[Whitney Melroy Greif]

Hello,

I just want to confirm what PRSice does when it says "Remove Ambiguous SNPs" when you run PRSice command line. Does this mean that variants that are in the target data, but not base data, are not included, and vice versa?

I want to make sure that if my base data has variants that are NOT present in my target data (e.g. when using summary statistics from the PGC there are a million plus variants, and I only have ~250,000 in my target data), this will not affect the output of PRSice.

Thank you,
Whitney

[Shing Wan Choi]

If the variants only present in the base but not the target file, then it will not be used. 

For remove ambiguous SNPs, we remove all A/T, G/C pairs as we cannot be sure how to flip them.