Imputation of 23andMe data

[Panacotaforcota]

I would like to impute data for a single person that was received from 23andMe platform. I used Michigan Imputation Server with the following settings:

Build: hg19
Reference Panel: [email protected] (hg19)
Population: eur
Phasing: eagle
Mode: imputation
Rsq filter: 0.3

As a result I got that almost all SNPs 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.

[jonathonl]

You should disable the Rsq filter for single sample imputation. Perfectly imputed hom ref and hom alts (i.e., HDS is 0,0 or 1,1) have no variation and would get filtered out.