Table 2 Evaluation of metrics for pipelines validation in high quality regions
From: Set-theory based benchmarking of three different variant callers for targeted sequencing
Variant caller | Metrics | ||||||||
|---|---|---|---|---|---|---|---|---|---|
TP | FP | FN | I | NAC | Recall | Precision | Frac_NA | F1Score | |
Freebayes | 233 | 3 | 0 | 2 | 23 | 1.000 | 0.987 | 0.089 | 0.989 |
VarScan | 233 | 18 | 0 | 2 | 60 | 1.000 | 0.928 | 0.193 | 0.959 |
Isaaca | 235 | 0 | 0 | 0 | 20 | 1.000 | 1.000 | 0.078 | 1.000 |