Table 2.
Large deletions (DELs) and insertions (INSs) (≥50 bp) calling performance across three HiFi data sets
| Library | Metric | FocalSV (target) | FocalSV (auto) | PAV | SVIM-asm | Dipcall | sawfish | cuteSV | SVIM | pbsv | Sniffles2 | SKSV | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| DEL | Hifi_L1 | Precision | 93.14% | 93.59% | 92.28% | 91.70% | 90.33% | 93.10% | 88.20% | 87.33% | 93.03% | 83.75% | 85.29% |
| Recall | 95.36% | 94.78% | 93.22% | 93.90% | 92.61% | 95.34% | 88.46% | 88.78% | 93.44% | 84.65% | 85.25% | ||
| F1 | 94.24% | 94.18% | 92.75% | 92.79% | 91.46% | 94.20% | 88.33% | 88.05% | 93.24% | 84.20% | 85.27% | ||
| GT concordance | 99.10% | 99.05% | 97.11% | 97.85% | 96.75% | 98.37% | 99.07% | 98.71% | 97.71% | 96.56% | 97.98% | ||
| Hifi_L2 | Precision | 92.65% | 93.81% | 92.04% | 92.01% | 90.11% | 93.34% | 93.83% | 82.90% | 92.21% | 92.67% | 85.81% | |
| Recall | 95.00% | 95.02% | 94.12% | 94.56% | 92.76% | 95.31% | 87.12% | 95.40% | 93.78% | 94.85% | 78.91% | ||
| F1 | 93.81% | 94.41% | 93.07% | 93.27% | 91.42% | 94.31% | 90.35% | 88.70% | 92.99% | 93.74% | 82.22% | ||
| GT concordance | 99.00% | 99.00% | 97.26% | 98.61% | 96.86% | 98.22% | 97.46% | 97.90% | 98.19% | 98.31% | 97.48% | ||
| Hifi_L3 | Precision | 92.67% | 93.71% | 91.71% | 91.70% | 89.94% | 93.15% | 94.23% | 75.30% | 92.49% | 92.81% | 85.88% | |
| Recall | 95.21% | 94.87% | 93.49% | 94.44% | 92.76% | 95.17% | 90.43% | 95.34% | 93.93% | 95.02% | 81.44% | ||
| F1 | 93.92% | 94.29% | 92.59% | 93.05% | 91.33% | 94.15% | 92.29% | 84.14% | 93.20% | 93.90% | 83.60% | ||
| GT concordance | 98.98% | 99.00% | 96.62% | 98.59% | 96.83% | 98.44% | 98.04% | 98.34% | 98.60% | 98.47% | 98.06% | ||
| Overall | Precision | 92.82% | 93.70% | 92.01% | 91.80% | 90.13% | 93.20% | 92.09% | 81.84% | 92.58% | 89.74% | 85.66% | |
| Recall | 95.19% | 94.89% | 93.61% | 94.30% | 92.71% | 95.27% | 88.67% | 93.17% | 93.72% | 91.51% | 81.87% | ||
| F1 | 93.99% | 94.29% | 92.80% | 93.04% | 91.40% | 94.22% | 90.32% | 86.96% | 93.14% | 90.61% | 83.70% | ||
| GT concordance | 99.03% | 99.02% | 97.00% | 98.35% | 96.81% | 98.34% | 98.19% | 98.32% | 98.17% | 97.78% | 97.84% | ||
| INS | Hifi_L1 | Precision | 90.80% | 88.50% | 86.30% | 86.50% | 72.80% | 83.89% | 87.50% | 85.10% | 90.00% | 79.00% | 86.10% |
| Recall | 93.90% | 93.88% | 93.10% | 93.10% | 91.40% | 94.24% | 82.30% | 69.60% | 77.40% | 76.80% | 86.60% | ||
| F1 | 92.40% | 91.11% | 89.60% | 89.70% | 81.00% | 88.76% | 84.90% | 76.60% | 83.20% | 77.90% | 86.40% | ||
| GT concordance | 98.10% | 98.39% | 95.60% | 97.80% | 77.80% | 92.38% | 99.10% | 90.00% | 87.70% | 89.30% | 98.30% | ||
| Hifi_L2 | Precision | 89.80% | 88.32% | 86.40% | 86.40% | 73.10% | 84.75% | 91.80% | 61.90% | 89.90% | 88.30% | 86.20% | |
| Recall | 93.80% | 93.77% | 93.30% | 92.90% | 91.60% | 94.05% | 82.40% | 91.60% | 76.70% | 91.80% | 61.70% | ||
| F1 | 91.70% | 90.96% | 89.70% | 89.50% | 81.30% | 89.16% | 86.80% | 73.90% | 82.80% | 90.00% | 71.90% | ||
| GT concordance | 98.30% | 98.20% | 96.10% | 97.70% | 78.50% | 92.95% | 97.60% | 94.00% | 95.40% | 97.00% | 97.70% | ||
| Hifi_L3 | Precision | 89.60% | 88.31% | 86.30% | 86.40% | 73.00% | 84.33% | 91.60% | 45.00% | 89.00% | 88.60% | 87.10% | |
| Recall | 93.80% | 93.88% | 93.00% | 93.20% | 91.80% | 94.04% | 86.00% | 92.10% | 76.70% | 92.80% | 71.00% | ||
| F1 | 91.70% | 91.01% | 89.50% | 89.60% | 81.30% | 88.92% | 88.70% | 60.50% | 82.40% | 90.70% | 78.20% | ||
| GT concordance | 98.50% | 98.41% | 94.90% | 98.00% | 78.30% | 92.45% | 98.40% | 94.30% | 96.20% | 97.10% | 98.60% | ||
| Overall | Precision | 90.07% | 88.38% | 86.33% | 86.43% | 72.97% | 84.32% | 90.30% | 64.00% | 89.63% | 85.30% | 86.47% | |
| Recall | 93.83% | 93.84% | 93.13% | 93.07% | 91.60% | 94.11% | 83.57% | 84.43% | 76.93% | 87.13% | 73.10% | ||
| F1 | 91.93% | 91.03% | 89.60% | 89.60% | 81.20% | 88.95% | 86.80% | 70.33% | 82.80% | 86.20% | 78.83% | ||
| GT concordance | 98.30% | 98.33% | 95.53% | 97.83% | 78.20% | 92.59% | 98.37% | 92.77% | 93.10% | 94.47% | 98.20% |
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The table presents recall, precision, F1 score (in %), and genotype accuracy (measured by genotype concordance) for all benchmarked SV callers. The highest scores for recall, precision, F1, and genotype accuracy are highlighted in bold. Additionally, the overall average performance for each SV type and library is summarized at the bottom of the table. Benchmarking was conducted using Truvari with the following parameter settings: p = 0.5, P = 0.5, r = 500, and O = 0.01.
