I impute some SNP that I have their real genotype by minimac3. I checked strand alignment and remove problematic SNPs and phased them by shapit. the result of imputation for rs... is AG , but the reall genotype in my data set is GA, or for another one imputed SNPs is CT but the real one is TC (while some of them are the same).
What is the reason? Is it because of a problem in my procedure? What should I do for that?
Thank you in advance for your help.