How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice

Question

[Aastha]

This is a two part question. First, when implementing PRSice, is there a way to make sure certain SNPs are retained for the PRS calculation? I basically want to avoid certain SNPs being removed during 'clumping'.. And second, if the SNP of interest is removed during clumping, is there a way to find out which SNP in LD is included (instead of the one I am interested in) in the PRS calculation?

Answer 1

[Sam]

1. You can "retain" a SNP of interest by manually setting their p-value at 0 (though that will also mean that you won't really be able to do p-value threshold)
2. If you want to check that, the best way is to "dry" run PRSice once with --no-clump --print-snp option, which will generate a .snp file. You can then clump your data set using PLINK with the --extract PRSice.snp option to obtain the information you wanted.