Hi there,

I am looking at calculating PRS for two groups vs UK biobank controls. One group has been WGS, whilst the other has been SNP array sequenced for the intention of GWAS approaches. I know ideally the data sets would be the same sequencing methods but it's just the data I have available.

I am wondering whats the best way to harmonise these data sets. I am assuming to strip back the WGS to the SNPs present in SNP array and then imputing all together, followed by running PCAmatchR to obtain ethnicity-matched controls. Has anyone done something like this before and do you have any tips or advice?

Many thanks in advance!!