List of used SNPs - Githubissues

privefl / bigsnpr

R package for the analysis of massive SNP arrays.

https://privefl.github.io/bigsnpr/

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Closed AbrahamVanDeWalle closed 10 months ago

AbrahamVanDeWalle commented 1 year ago

Hi!

I was wondering if, when calculating PRS using LDpred2, it was possible to obtain a list of all the used SNPs in the PRS calculation.

Kind regards, Bram

privefl commented 1 year ago

All the variants you provide as input (in e.g. df_beta) are used.