I ran Minimac4 to do imputation on the basis of ~750,000 loci that were genotyped. The reference panel I used was 1000 genome. In the output files, I found that the genotype data at some typed loci changed compared with the input files. For example, Sample 1 was genotyped CC at the locus rs1058164, but in the Minimac output, it is GC at the same locus.
Does this make sense? I used to assume all the typed loci wouldn't be changed by imputation.
Any help is appreciated!