Table 3.
True positive (TP), false positive (FP) and TP/FP ratio for short CNVs (1–4 exons)
| Program | 1000 genomes exomes | Primary immunodeficiency patients | ||||
|---|---|---|---|---|---|---|
| TP | FP | TP/FP ratio | TP | FP | TP/FP ratio | |
| CONIFER | 0 | 0 | 4 | 6 | 0.67 | |
| XHMM | 0 | 4 | 7 | 32 | 0.22 | |
| ExomeDepth | 0 | 2 | 50 | 301 | 0.17 | |
| ExomeCopy | 914 | 6591 | 0.14 | 161 | 1076 | 0.15 |
| ExCopyDepth | 63 | 267 | 0.24 | 52 | 669 | 0.08 |
| Intersection of ExomeCopy/ExCopyDepth | 34 | 76 | 0.45 | 44 | 478 | 0.09 |
TP, True positive CNVs (CNVs identified both exaCGH and computational programs); FP, False positive CNVs (CNVs identified only by computational programs but not by exaCGH); TP/FP ratio, Ratio between true positive and false positive CNVs.