Table 1.
Simulation results on GRCh37
| Tool | No. calls | TP | FP | FN | found | precision | recall |
|---|---|---|---|---|---|---|---|
| Inversions > 40 Kbp (n = 275) | |||||||
| DELLY | 780 | 461 | 319 | 19 | 256 | 59.10% | 96.04% |
| LUMPY | 174 | 174 | 0 | 84 | 191 | 100.00% | 67.44% |
| GASVPro | 475 | 9 | 166 | 266 | 9 | 1.89% | 3.83% |
| Valor | 198 | 191 | 7 | 54 (28)a | 221 | 96.46% | 77.96% (87.21%b) |
| Inversions > 80 Kbp (n = 167) | |||||||
| DELLY | 589 | 274 | 315 | 15 | 152 | 46.52% | 94.81% |
| LUMPY | 95 | 95 | 0 | 61 | 106 | 100.00% | 60.90% |
| GASVPro | 404 | 5 | 399 | 164 | 3 | 1.24% | 2.96% |
| Valor | 131 | 124 | 7 | 28 (8)a | 139 | 94.66% | 81.58% (93.94%b) |
We implanted 686 inversions to the reference genome (GRCh37) using VarSim and simulated two libraries, one pooled fosmid clone sequencing library for Valor, and one WGS data set. 275 inversions had size >40 Kbp, and 167 were >80 Kbp. a26 inversions (>40 Kbp) and 20 inversions (>80 Kbp) had no clone coverage. bwhen inversions that had no clone coverage at breakpoints are removed. TP true positive, FP false positive, FN false negative. found: number of simulated inversions that intersect (>50% reciprocal) with calls. Precision: positive predictive value, calculated as TP/(TP + FP). Recall: sensitivity, calculated as TP/(TP + FN). Note that due to diploid simulated inversions, one call may intersect with multiple implanted inversions