I imputed genotypes for a single person using Michigan Imputation Server. I used the following settings:
- Build: hg19
- Reference Panel: email@example.com (hg19)
- Population: eur
- Phasing: eagle
- Mode: imputation
- Rsq filter: 0.3
As a result, almost all SNP were imputed as heterozygotes. I found this strange, because before, when I used this server to impute something else, some cohort of data, I have never met such problem.
How can I explain this situation and how I can fix it? Maybe some of you faced it.