TABLE II.
Imputation yield using the fixed error rate approach
| Software | Phase II Reference Panela | Threshold b | Yield |
|---|---|---|---|
| BEAGLE | CEU | 0.967 | 575 |
| YRI | 0.824 | 1,976 | |
| Unweighted CEU+YRI | 0.832 | 3,847 | |
| MACH | CEU | 0.999 | 3,121 |
| YRI | 0.688 | 13,927 | |
| Unweighted CEU+YRI | 0.946 | 10,341 | |
| Weighted CEU+YRI | 0.939 | 9,025 | |
| PLINK | CEU | NA | 0 |
| YRI | NA | 0 | |
| Unweighted CEU+YRI | NA | 0 |
Error rates were fixed at 10% for these analyses.
The phase II CEU and YRI reference panels both consist of 60 founders. The unweighted CEU+YRI panel consists of all 120 CEU and YRI founders in a single reference panel. A weighted CEU+YRI reference panel consisted of 48 randomly chosen YRI founders and 12 randomly chosen CEU founders consistent with observed admixture proportions of ~80% and ~20%, respectively. Results shown for the weighted panel approach are averages of 30 randomly generated panels.
Threshold indicates the minimum posterior probability for imputing discrete genotype calls to achieve concordance between imputed and observed genotypes of 0.90, equivalent to a fixed 10% error rate. NA indicates that the program could not achieve concordance of 0.90 using the reference panel.