Table 1.
Comparison of Methods for Single-Cell Haplotyping and Genotype Inference
|
Single-Cell Haplotyping | ||
|---|---|---|
| Algorithm | Accuracya | Coverageb |
| siCHILD (1D-MF) | 99.71% (±0.09% SD) | 98.82% (±0.16% SD) |
| siCHILD (haplarithmisis) | 99.99% (±0.02% SD) | 96.16% (±0.35% SD) |
| Merlin (–best) | 88.24% (±1.88% SD) | 91.16% (±0% SD) |
| Merlin (–error and–best) | 94.46% (±1.22% SD) | 91.16% (±0% SD) |
| Single-Cell Genotype Inference | ||
| Algorithm | Accuracyc | Coveraged |
| GenCall | 90.57% (±1.75% SD) | 58.8% (±1.82% SD) |
| siCHILD (1D-MF) | 98.84% (±0.06% SD) | 98.95% (±0.19% SD) |
| siCHILD (haplarithmisis) | 99.07% (±0.05% SD) | 91.71% (±0.56% SD) |
| 1D-MF and haplarithmisis consensus | 99.08% (±0.03% SD) | 91.22% (±0.54% SD) |
Average accuracies of maternal haplotypes in single cells to their matching multi-cell DNA sample. Specifically, to compute the accuracies, the single-cell Merlin-inferred haplotypes were compared with multi-cell Merlin-inferred haplotypes; and similarly, single-cell siCHILD-inferred haplotypes were compared with multi-cell siCHILD-inferred haplotypes. As a control, the concordance between multi-cell siCHILD-inferred haplotypes and multi-cell Merlin-inferred haplotypes is >99.99%.
Percentage of SNPs genome wide with a haplotype call.
Average accuracies of inferred genotypes of single cells to the multi-cell DNA genotype.
Percentage of SNPs genome wide with an inferred genotype call.