Dear users, I am new to GWAS study, I have a concern about genetic association procedures. After having real genotyped data from the experiment ( we use the array for genotyping), we need to impute the genotype data. However, I am quite confused that how to do genetic association for the imputed data. I read a paper in which they use different packages in R to analyze the genetic association with real genotyped data and imputed genotyped data. Other people say they combine real genotyped data and imputed genotype data and base on some criteria to filter the imputed SNP with low quality (like infor score to filter the SNP) Could anyone can share your experience about this? How do you often do in this case? Thank you very much.