Table 2 Sensitivity/Specificity comparison with other variant detection methods
NRAF | Median | SAMtools | GATK | CRISP | VarScan2 | VarScan2 | Strelka | SNVer | MuTect | RVD2 | RVD2 |
|---|---|---|---|---|---|---|---|---|---|---|---|
depth | mpileup | somatic | MCMC | Variational | |||||||
0.1% | 39 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/0.99 | 0.00/1.00 | 0.00/1.00 |
408 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.07/0.92 | 0.00/1.00 | 0.00/1.00 | 0.29/0.91 | 0.00/1.00 | 0.07/1.00 | |
4129 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.57/0.52 | 0.00/1.00 | 0.00/1.00 | 0.64/0.86 | 0.14/1.00 | 0.29/1.00 | |
41449 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.64/0.79 | 0.00/1.00 | 0.00/1.00 | 0.14/0.93 | 0.86/0.97 | 1.00/1.00 | |
0.3% | 36 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.43/1.00 | 0.00/1.00 | 0.00/1.00 |
410 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.21/0.95 | 0.00/1.00 | 0.00/1.00 | 0.50/0.94 | 0.00/1.00 | 0.00/1.00 | |
4156 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.57/0.53 | 0.00/1.00 | 0.21/0.99 | 0.36/0.91 | 1.00/0.99 | 1.00/0.98 | |
41472 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.64/0.75 | 0.00/1.00 | 0.86/0.97 | 0.43/0.90 | 1.00/0.85 | 0.93/0.91 | |
1.0% | 53 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/0.99 | 0.00/1.00 | 0.00/1.00 | 0.29/0.98 | 0.00/1.00 | 0.00/1.00 |
535 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.43/0.89 | 0.00/1.00 | 0.29/1.00 | 0.71/0.91 | 0.21/1.00 | 0.29/1.00 | |
5584 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.57/0.47 | 0.00/1.00 | 1.00/0.99 | 0.64/0.95 | 1.00/0.98 | 1.00/0.98 | |
55489 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.00/1.00 | 0.64/0.69 | 0.00/1.00 | 1.00/0.97 | 0.86/0.90 | 1.00/0.87 | 0.93/0.95 | |
10.0% | 22 | 0.21/1.00 | 0.43/1.00 | 0.86/1.00 | 0.00/1.00 | 0.36/1.00 | 0.29/1.00 | 0.93/1.00 | 0.86/0.99 | 0.00/1.00 | 0.57/1.00 |
260 | 0.00/1.00 | 0.57/1.00 | 1.00/1.00 | 0.00/1.00 | 0.86/1.00 | 1.00/1.00 | 1.00/1.00 | 1.00/0.99 | 1.00/1.00 | 1.00/1.00 | |
2718 | 0.00/1.00 | 0.79/1.00 | 0.07/1.00 | 0.00/1.00 | 0.57/0.78 | 1.00/1.00 | 1.00/0.99 | 1.00/0.98 | 1.00/1.00 | 1.00/1.00 | |
26959 | 0.00/1.00 | 0.57/1.00 | 0.00/1.00 | 0.00/1.00 | 0.64/0.53 | 1.00/0.99 | 1.00/0.98 | 1.00/0.98 | 1.00/1.00 | 1.00/1.00 | |
100.0% | 27 | 1.00/0.99 | 1.00/1.00 | 1.00/1.00 | 1.00/1.00 | 1.00/1.00 | 1.00/1.00 | 1.00/0.99 | 1.00/0.98 | 1.00/1.00 | 1.00/1.00 |
298 | 1.00/0.99 | 1.00/1.00 | 1.00/1.00 | 1.00/1.00 | 1.00/0.99 | 1.00/0.99 | 1.00/0.98 | 1.00/0.98 | 1.00/1.00 | 1.00/1.00 | |
3089 | 0.86/1.00 | 1.00/1.00 | 1.00/0.99 | 1.00/1.00 | 1.00/0.65 | 1.00/0.99 | 1.00/0.98 | 1.00/0.98 | 1.00/1.00 | 1.00/1.00 | |
30590 | 0.71/1.00 | 1.00/1.00 | 1.00/1.00 | 1.00/1.00 | 1.00/0.39 | 1.00/1.00 | 1.00/0.98 | 1.00/0.99 | 1.00/1.00 | 1.00/1.00 |