Table 1 General metrics for three variant calling pipelines
From: Set-theory based benchmarking of three different variant callers for targeted sequencing
Metrics | Variant calling pipeline | ||
|---|---|---|---|
Isaac | Freebayes | VarScan | |
Number of variants (SNP) | 255 | 259 | 311 |
Variant rate | 1/1 121 0146 | 1/11 633 348 | 1/9 799 651 |
Ts/Tv | |||
Transitions (Ts) | 204 | 208 | 241 |
Transversions (Tv) | 51 | 51 | 70 |
Ts/Tv ratio | 4.00000 | 4.07841 | 3.4429 |
Functional class | |||
Missense | 218 | 237 | 321 |
Silent | 495 | 499 | 507 |
Missense/silent ratio | 0.4404 | 0.4749 | 0.6331 |