Table 4. Sarek WGS germline variant benchmarking.
Summary of accuracy measures for the two variant callers used in Sarek to detect germline single-nucleotide variants (SNVs) and germline insertion/deletion variants (INDELs), as well as their union and intersection.
| Germline caller | Recall | Precision | F1-score |
|---|---|---|---|
| SNV (Gold Set: n=3088156) | |||
| GATK4 HaplotypeCaller | 0.93 | 1.00 | 0.96 |
| Strelka2 | 0.98 | 1.00 | 0.99 |
| Union (GATK4 HaplotypeCaller, Strelka2) | 0.99 | 0.94 | 0.96 |
| Intersection (GATK4 HaplotypeCaller, Strelka2) | 0.93 | 1.00 | 0.96 |
| INDEL (Gold Set: n=530423) | |||
| GATK4 HaplotypeCaller | 0.91 | 0.99 | 0.95 |
| Strelka2 | 0.92 | 0.99 | 0.95 |
| Union (GATK4 HaplotypeCaller, Strelka2) | 0.93 | 0.98 | 0.96 |
| Intersection (GATK4 HaplotypeCaller, Strelka2) | 0.90 | 1.00 | 0.94 |