Table 1 Performance summary ClinSV. Summary of ClinSV’s performance by metric, variant type, and size. Input variants were pass and high confidence. Determining the false positive rate and false negatives, input variants were further visually reviewed prior the performance analysis
Metric | Reference data or technology | Preceding visual review | Value | Results table |
|---|---|---|---|---|
Sensitivity | Simulated ClinVar |  |  | Table 2 |
 Deletions | No | 99.7% > 10 kb 88.2% < 10 kb |  | |
 Duplications | No | 100.0% > 10 kb 63.4% < 10 kb |  | |
GIAB1 | Â | Â | Â | |
 Deletions | No | 97.1% > 10 kb 87.8% < 10 kb | Additional file 1: Table S7 | |
GIAB2 | Â | Â | Â | |
 Deletions | No | 97.0% > 10 kb 71.4% < 10 kb | Additional file 1: Table S8 | |
 Duplications | No | 100.0% > 10 kb 2.3% < 10 kb | Additional file 1: Table S9 | |
Microarray | No | 100% pathogenic CNVs > 99% any CNVs |  | |
False positive rate | PacBio data | Yes | 1.5% 4.5% incl. inconclusive | Additional file 1: Table S10 |
MLPA | Yes | 0% 10% incl. Inconclusive | Additional file 1: Table S11 | |
False negatives | MLPA | Yes | 30% | Additional file 1: Table S13 |
Reproducibility | WGS | No | 99.1% high CNVs 83.9% high and pass SVs | Table 3 |