Quality control on imputed genotypes for GWAS / application of PGS

Question

[loy_loy]

Hi everyone,

I want to run a GWAS on imputed genotypes from UKB. Unfortunately, I only found tutorials that describe the quality control of genotypes in preparation for a GWAS. Are there tutorials for imputed datasets? I suppose that a lot of QC steps are already performed before imputation. Maybe somebody has advice for me or knows a good tutorial or publication with well-documented methods on this topic.

Thank you!

Lynn

[bk11]

Post imputation, basically the quality control steps for imputed data will the same as for the genotyped data pre-imputation. However, based on your imputation method, you need to define imputation quality threshold (for e.g., R2 if data had been imputed from TOPMed or Michigan Imputation Servers) to filter out the low quality imputed variants. In general you can follow the QC steps discussed in this paper.

[loy_loy]

Thank you very much for your answer! I already performed QC according to this paper on genotypes and was very happy with it because of the clear writing style and the available scripts.