When using PRSice for PRS calculation of target data using a file of variants from the PGS catalog, does the variant file from the PGS catalog replace the GWAS summary statistics (referred to as "base data" in the tutorial)?
I had previously found this similar question: https://www.biostars.org/p/407615/, but just making sure that the list of PRS variants replaces the summary statistics/base data.
Thanks in advance.
1 answer
As long as it has the SNP, Effective allele, effect size and p-value column, then it is fine. If there isn't a p-value column, you can sometimes make a "fake" p-value column with all 1s or all 0s. Depending on the data, you might also want to skip clumping and thresholding.
Sam
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