How to check the imputation quality of genotyping files?
Dear talents,
Hi,
I recently started a GWAS project with genotyping files (Oncoarray and iCOGS if you have heard) which has been imputed by previous colleague who has left. I have the imputation code from him.
In addition to examine the imputation code, how can I have a fast check of the quality of imputed genotyping files themseleves?
Thank you very much.
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how was it imputed, usually the softwares give an estimated imputation quality metric for each variant in the output