I downloaded imputed .bgen and .sample files from UKBiobank and now I am planning to do GWAS in it. I plan to use Plink2.
can you please tell me which QC steps I would have to perform?
I was thinking to do these:
-remove related individuals -remove non EUR -remove SNPs with minor allele freq < 0.001 -model using ancestry info
Is there is some standard pipeline to do this in Plink2 or some related files from UKBiobank?