Missing snps in PRSice

Question

[joanfitz5]

Hi, I am running a PRS analysis with PRSice and am using a base file of 96 snps that are already clumped. The output says that 15 snps in the list are missing from the target file but I can find them in the bim file using grep. Is there a reason that PRSice reports them as missing?

[Lemire]

Could they be A/T and C/G SNPs? Those are excluded by PRSice. Without knowledge of strand, the risk allele can't be determined.

[joanfitz5]

Thanks Lemire - that explains it thanks!

[Kevin Blighe]

add prsice tag