Table 6.
The averaged performance of GATK and GATKcan in detecting mutations of 27,167 called variants (of 432 genes) from exome-seq of 215 TCGA OC tumors, checked against the reported mutations by TCGA.
| GATK | GATKcan (s.e.) | Mutect | VarScan 2 | ||
|---|---|---|---|---|---|
| trained by | |||||
| 10 tumors | 44 tumors | ||||
| TPR§ | 85.2 | 89.1 (1.1) | 89.7 (0.7) | — | — |
| cFPR | 70.4 | 5.0 (0.2) | 5.1 (0.3) | — | — |
| precision | 2.9 | 30.5 (1.1) | 30.1 (1.4) | — | — |
| MCC | 5.0 | 50.4 (1.2) | 50.2 (1.4) | — | — |
| TPR†§ | 98.2 | 98.2 (0.0) | 98.2 (0.0) | 100.0 | 100.0 |
| cFPR† | 86.9 | 4.1 (1.2) | 3.9 (0.8) | 34.5 | 23.8 |
| precision† | 34.2 | 91.7 (2.1) | 92.0 (1.4) | 62.5 | 65.9 |
| MCC† | 17.9 | 92.5 (1.7) | 92.7 (1.1) | 64.0 | 70.9 |
Next, the four algorithms identified mutations from 178 somatic variants, on which TPR†, cFPR†, precision† and MCC† were computed. §The unit of all performance measures and their s.e.’s are %.