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?
Entirely depends on the study. I would recommend thinking about what you're trying to accomplish and exploring the literature for meaningful filtering approaches depending on what you want to do.
yes I agree, and I mentioned above those 4 QC steps I plan to do. My question is more how to do this in Plink2? or some other software?
For example to deal with MAF I would do this: plink2 --bgen ukb_imp_chr17_v3.bgen ref-first --sample ukb44316_imp_chr17_v3_s487317.sample --maf 0.001 --make-bpgen --out chr17
But I don't know how to deal with the rest of 3 QC steps. Also I should mentioned this is imputed data from UKBiobank.
Hi! Did you manage to solve this?