Closed:Polygenic risk score: before or after SNP filtering?

Question

[aldoc]

Hi,

I have to calculate the Polygenic Risk Score (PGRS) for a certain phenotype, on two different datasets.

Initially, both datasets contain the same markers, but filtering by MAF/HWE would leave a different subset in each case. I'm thus wondering how to do that filtering (if needed). These are the options:

• Estimating PGRS in each dataset, without any MAF/HWE filtering
• Merging both datasets, filtering by MAF/HWE, and then computing PGRS
• Filtering each dataset by MAF/HWE, re-filtering to leave only SNPs shared across datasets, and then computing PGRS
• Other...

I guess there are some standard guidelines for this, but I haven't found the right references. Any help is appreciated.

Thanks in advance,