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Missing snps in PRSice

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?

snp prsice
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updated by Kevin Blighe Kevin Blighe • written by joanfitz5 • joanfitz5

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.

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written by Lemire Lemire

Thanks Lemire - that explains it thanks!

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written by joanfitz5 • joanfitz5

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