Table 4.
The averaged performances of GATK, GATKcan (trained by ten & 44 EC tumors), VarScan 2 and MuTect in detecting mutations from ~2,102 (~1,741) somatic variants of 231 (197) randomly sampled endometrial tumors in ten repeats, checked against the TCGA reported mutations.
| Test set | GATK | GATKcan | Mutect | VarScan 2 | ||
|---|---|---|---|---|---|---|
| 231 samples | TPR†§ (s.e.) | 98.8 (0.0) | 98.6 (0.6) | -----*----- | 94.3 (0.1) | 99.6 (0.0) |
| cFPR† (s.e.) | 81.0 (0.4) | 5.7 (0.4) | -----*----- | 37.9 (0.5) | 60.5 (0.7) | |
| precision† (s.e.) | 54.7 (0.3) | 94.4 (0.3) | -----*----- | 71.1 (0.2) | 61.9 (0.2) | |
| MCC† (s.e.) | 29.4 (0.4) | 92.9 (0.5) | -----*----- | 59.5 (0.4) | 48.9 (0.5) | |
| 197 samples | TPR†§ (s.e.) | 98.8 (0.3) | 98.5 (1.0) | -----*----- | 94.1 (1.0) | 99.6 (0.1) |
| cFPR† (s.e.) | 80.2 (2.3) | 6.1 (0.9) | -----*----- | 36.8 (5.2) | 59.6 (4.5) | |
| precision† (s.e.) | 55.0 (0.7) | 94.2 (0.6) | -----*----- | 71.9 (2.1) | 62.4 (0.9) | |
| MCC† (s.e.) | 30.3 (1.5) | 92.5 (0.3) | -----*----- | 60.3 (3.5) | 49.5 (3.1) |
†Adjusted performance measures. §The unit of all performance measures and their s.e.’s are %. *The P value of the two sample t-test between GATKcan and MuTect < 10−8.