Table 2 Comparison of four approaches on mutations using simulated WES data
From: 2-kupl: mapping-free variant detection from DNA-seq data of matched samples
Mutations | 2-kupl | DiscoSNP++ | Lancet | GATK-MuTect2 |
|---|---|---|---|---|
True positive | 581 | 373 | 604 | 689 |
False positive | 45 | 3 | 126 | 2 |
False negative | 241 | 530 | 218 | 133 |
Recall | 0.71 | 0.41 | 0.73 | 0.84 |
FDR | 0.07 | 0.01 | 0.17 | 0.003 |
Precision | 0.93 | 0.99 | 0.83 | 0.997 |
F1 score | 0.80 | 0.58 | 0.78 | 0.91 |