Table 3.
Results from synthetic data
| Caller | TP | FP | TN | FN | F-meas | MCC | FP Germlines | FP Wild-types |
|---|---|---|---|---|---|---|---|---|
| JointSNVMix1 (Trained) | 140 | 13 | 999788 | 59 | 0.795 | 0.802 | 8 | 2 |
| JointSNVMix1 | 153 | 50 | 999751 | 46 | 0.761 | 0.761 | 42 | 0 |
| SNVMix1 (Trained) | 190 | 823 | 998978 | 9 | 0.314 | 0.423 | 743 | 70 |
| Joint Fisher | 159 | 1155 | 998646 | 40 | 0.21 | 0.311 | 1109 | 0 |
| SNVMix1 | 178 | 1653 | 998148 | 21 | 0.175 | 0.295 | 1632 | 0 |
| Independent Fisher | 159 | 2538 | 997263 | 40 | 0.11 | 0.217 | 2464 | 0 |
We report the number of true positives (TP), false positives (FP), true negatives (TN), false negatives (FN), F-measure (F-meas), Matthews correlation coefficients (MCC), false positives which are germline (FP Germlines), and false positives which are wild-type (FP Wild-types). The best results for each category are shown in bold.