Table 3.
Comparison of performance between bioinformatic tools according to MCC
| Bioinformatic tool or combination of tools | True Positives | True Negatives | False Positives | False Negatives | MCC | % of total variants mispredicted (FN+FP) | % of total variants discordant between tools |
|---|---|---|---|---|---|---|---|
| PolyPhen-2 | 222 | 44 | 27 | 25 | 0.524 | 16.35 | NA |
| SIFT | 231 | 42 | 29 | 16 | 0.568 | 14.15 | NA |
| REVEL (≥0.5) | 237 | 42 | 29 | 10 | 0.620 | 12.26 | NA |
| SIFT + PolyPhen-2 | 218 | 35 | 20 | 12 | 0.621 | 10.06 | 10.38 |
| Optimized Align-GVGD (≥C15) | 220 | 54 | 17 | 27 | 0.622 | 13.84 | NA |
| Optimized Align-GVGD (≥C15) + PolyPhen-2 | 211 | 41 | 14 | 16 | 0.666 | 9.43 | 11.32 |
| Optimized Align-GVGD (≥C15) + SIFT + PolyPhen-2 | 208 | 34 | 13 | 12 | 0.675 | 7.86 | 16.04 |
| BayesDel (≥0.16) | 218 | 60 | 11 | 29 | 0.675 | 12.58 | NA |
| Optimized Align-GVGD (≥C15) + SIFT | 217 | 40 | 15 | 13 | 0.680 | 8.81 | 10.38 |
| Optimized Align-GVGD (≥C15) + REVEL (≥0.5) | 219 | 42 | 16 | 9 | 0.719 | 7.86 | 10.06 |
| Optimized Align-GVGD (≥C15) + BayesDel (≥0.16) | 209 | 49 | 6 | 18 | 0.756 | 7.55 | 11.32 |