Table 7 Optimized F1-scores of calls for each variant caller considering FF sample as gold standard (UZ001). Optimized F1-scores of calls made by each variant caller considering FF sample as gold standard
From: Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples
Caller - threshold | FF (gold std.) | FFPE | Overlap | Sensitivity | Precision | F1-score |
|---|---|---|---|---|---|---|
Strelka2–9.5 | 4656 | 4559 | 3316 | 0.7122 | 0.7274 | 0.7197 |
Mutect2–13 | 4656 | 5658 | 3418 | 0.7341 | 0.6041 | 0.6628 |
VarScan2–0.00995 | 4656 | 1755 | 425 | 0.1045 | 0.2422 | 0.1460 |
Shimmer – 0.0495 | 4656 | 262 | 16 | 0.0197 | 0.0611 | 0.0298 |