Table 2.
True positive (TP)/false positive (FP) CNV ratio predicted from each program
| Program | AvgTP | TP/FP ratio | Total CNV count 3 | Average CNVs per sample 4 |
|---|---|---|---|---|
| CoNIFER | 1.33 (1.33)1 | 0.92 (1.09)2 | 23 | 2.56 |
| ExCopyDepth | 28.11 (15.86)1 | 0.34 (0.51)2 | 422 | 46.89 |
| ExomeCopy | 289.33 (226.0)1 | 0.20 (0.21)2 | 11978 | 1330.89 |
| ExomeDepth | 1.11 (0.78)1 | 0.67 (0.70)2 | 17 | 1.89 |
| Intersection of ExomeCopy / ExCopyDepth | 12.89 (7.33)1 | 0.28 (0.33)2 | 218 | 24.22 |
| XHMM | 4.44 (3.56)1 | 0.32 (0.53)2 | 92 | 10.22 |
| CONTRA | 17.88 (16.56)1 | 0.20 (0.20)2 | 896 | 99.56 |
TP/FP ratio for each program was calculated using CNVs identified from 9, 1000 genomes samples run in both computational programs and exaCGH; Average true positive (AvgTP) = TP/9; TP/FP ratio = TP CNV count /FP CNV count; Average CNVs per sample = Total CNV count/9.
1Average true positive calculated by excluding CNVs in X and Y Chromosomes.
2TP/FP ratio calculated by excluding CNVs in X and Y Chromosomes.
3Total number of CNVs predicted by each program excluding CNVs in X and Y Chromosomes (CNV counts for each program including X and Y Chromosomes are presented in Figure 1b).
4Average CNVs per sample calculated from counts presented in total CNV count column in Table 2.