From Genome Analysis Wiki
→How do I get imputation quality estimates?
Estimated per allele error rate is 0.0293
A better approach is to mask a small proportion of SNPs (vs. genotypes in the above simple approach). One can generate a mask.dat from the original .dat file by simply changing the flag of a subset of markers from M to S2 without duplicating the .ped file. Post-imputation, one can use [http://genome.sph.umich.edu/wiki/CalcMatch CalcMatch ]and [http://csg.sph.umich.edu//ylwtx/doseR2.tgz doseR2.pl ]to estimate genotypic/allelic error rate and correlation respectively. Both programs can be downloaded from [http://csg.sph.umich.edu//ylwtx/software.html http://
'''Warning''': Imputation involving masked datasets should be performed separately for imputation quality estimation. For production, one should use all available information.