Table 1.
Performance of CNV detection in the experimental data analysis for NA12156 and NA12878.
| Sample(s) | Algorithm | CNV bases | CNV regions | Sample(s) | Algorithm | CNV bases | CNV regions | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| bpa | Recall | FPR | Precision | Regionb | Detection rate | bpa | Recall | FPR | Precision | Regionb | Detection rate | ||||
| Single-sampleanalysis (NA12156) | CONY | 371,984 | 91.34% | 9.71% | 1.68% | 33 | 91.67% | Single-sample analysis (NA12878) | CONY | 202,607 | 91.43% | 0.51% | 1.65% | 25 | 83.33% |
| CNVnator | 343,308 | 84.30% | 13.07% | 1.15% | 25 | 69.44% | CNVnator | 168,094 | 75.86% | 0.54% | 1.31% | 11 | 36.67% | ||
| FREEC | 86,204 | 21.17% | 11.19% | 0.34% | 2 | 5.56% | FREEC | 124,272 | 56.08% | 0.46% | 1.13% | 2 | 6.67% | ||
| rdxplorer | 284,865 | 69.95% | 2.28% | 5.27% | 11 | 30.56% | rdxplorer | 119,034 | 53.72% | 2.17% | 0.23% | 7 | 23.33% | ||
| DGV | 407,253 | 36 | DGV | 221,597 | 30 | ||||||||||
| Paired-samples analysis (Case:NA12156/ Control:NA12878) | CONY | 376,510 | 73.10% | 0.74% | 18.55% | 23 | 63.89% | Paired- samples analysis (Case:NA12878/ Control:NA12156) | CONY | 355,947 | 69.11% | 4.57% | 0.32% | 25 | 69.44% |
| CNVSeq | 163,695 | 31.78% | 15.44% | 0.47% | 29 | 80.56% | CNVSeq | 175,150 | 34.00% | 0.50% | 1.48% | 33 | 91.67% | ||
| FREEC | 178,282 | 34.61% | 6.63% | 1.18% | 3 | 8.33% | FREEC | 230,142 | 44.68% | 1.62% | 0.59% | 6 | 16.67% | ||
| DGV | 515,073 | 36 | DGV | 515,073 | 36 | ||||||||||
aThe number of CNV basepairs in the DGV that are also identified by the algorithm.
bThe number of CNV regions in the DGV that have any position identified as a CNV via the algorithm.