Table 2 Performance of smCounter, MuTect, and VarDict in detecting 1% variants in the coding region of N0030. Cutoffs were selected to represent optimal performance
Variant type | Variant Caller | TP | FP | FN | TPR(%) | FP /Mb | PPV(%) |
|---|---|---|---|---|---|---|---|
SNV | smCounter | 205 | 7 | 18 | 91.9 | 10 | 96.7 |
| Â | MuTect | 214 | 58 | 9 | 96.0 | 85 | 78.7 |
| Â | VarDict | 204 | 169 | 19 | 91.5 | 248 | 54.7 |
INDEL | smCounter | 45 | 5 | 4 | 91.8 | 7 | 90.0 |
| Â | VarDict | 43 | 100 | 6 | 87.8 | 147 | 30.1 |