Table 3.
The averaged performances of GATK and GATKcan in detecting mutations from (A) ~61,507 variants of randomly sampled 231 endometrial tumors in ten repeats, and (B) ~52,291 variants of randomly sampled 197 endometrial tumors in ten repeats, checked against the 184,824 reported mutations in EC of TCGA.
| GATK | GATKcan | |||
|---|---|---|---|---|
| A. | ||||
| Training | TPR§ (s.e.) | — | -----*----- | 99.0 (1.0) |
| cFPR (s.e.) | — | -----*----- | 11.9 (1.3) | |
| Test | TPR (s.e.) | 88.2 (0.6) | -----*----- | 96.1 (1.9) |
| cFPR (s.e.) | 65.2 (0.1) | -----*----- | 12.2 (1.6) | |
| precision (s.e.) | 12.6 (0.4) | -----*----- | 46.0 (3.2) | |
| MCC (s.e.) | 14.5 (0.5) | -----*----- | 61.8 (2.0) | |
| B. | ||||
| Training | TPR§ (s.e.) | — | -----*----- | 98.8 (0.5) |
| cFPR (s.e.) | — | -----*----- | 12.1 (1.6) | |
| Test | TPR (s.e.) | 88.1 (1.3) | -----*----- | 96.1 (2.1) |
| cFPR (s.e.) | 64.9 (0.4) | -----*----- | 12.3 (1.6) | |
| precision (s.e.) | 12.6 (0.9) | -----*----- | 45.6 (2.9) | |
| MCC (s.e.) | 14.6 (1.0) | -----*----- | 61.4 (1.8) | |
§The unit of all performance measures and their s.e.’s are %. *Denotes the P value of the two sample t-test < 10−7.