Number of SNPs included in the PRS calculation (PRSice)

Question

[hello_genome]

I have a doubt about the actual number of SNPs that were used for the PRS calculation using PRSice v2. Is it equal to the "Number of variant(s) after clumping : 104,246" from the log file, or to the number in the column "Num_SNP" (= 1,058) of the summary output file?

Answer 1

[Sam]

That will be the Num SNP. The number of variants after clumping is exactly that, the number of variants after clumping, but not the number of variants included in the final PRS.

[hello_genome]

Thank you!