PRS using PGS Catalog

Question

[Humza]

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.

Answer 1

[Sam]

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

[Humza]

Thanks, Sam!

[Jenish]

Does the --chr-id option not work when there are no SNP IDs?

[Sam]

It was designed to work when there are no SNP IDs. Though the current implementation is a bit iffy (e.g. it doesn't work well if you are doing SNP selection). We are trying to improve it, but that should take us a long time to reach the first beta version.