Table 1. Comparison of various mappers for SNV calling.
| LAST | marginAlign | BWA-MEM | BLASR | DALIGNER | GraphMap | |
|---|---|---|---|---|---|---|
| Precision (%) | 94 | 100 (36) | 96 | 100 | 93 | 96 |
| True positives | 49 | 1 (107) | 47 | 43 | 75 | 86 |
Results are based on amplicon sequencing data for a human cell line (NA12878) for the genes CYP2D6, HLA-A and HLA-B. Precision values are likely to be an underestimate of what can be expected genome-wide due to the repetitive nature of the regions studied and the incompleteness of the gold-standard set. Results for marginAlign using marginCaller are shown in parentheses.