Table 3.
The performance comparison of PyroHMMvar with PyroHMMvar-SW, which replaces the HMM with a homopolymer-aware Smith–Waterman alignment method, and PyroHMMvar-Unique, which uses the unique read sequences as the consensus sequences instead of the weighted alignment graph
| Method | SNP |
Indel |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| TP | FP | SEN (%) | SPE (%) | F1 (%) | TP | FP | SEN (%) | SPE (%) | F1(%) | |
| PyroHMMvar | 28 393 | 325 | 80.9 | 98.9 | 89.0 | 2 608 | 092 | 59.2 | 96.6 | 73.4 |
| PyroHMMvar-SW | 28 297 | 340 | 80.6 | 98.8 | 88.8 | 2 285 | 263 | 51.8 | 89.7 | 65.7 |
| PyroHMMvar-Unique | 21 224 | 126 | 60.5 | 99.4 | 75.2 | 1 723 | 018 | 39.1 | 99.0 | 56.0 |