Table 6 PSE-HMM is compared to other tools in detecting genome-wide deletions and tandem duplications of size 1Â kb, 3Â kb, and 5Â kb
| Â | CNV length | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
1Â kb | 3Â kb | 5Â kb | ||||||||
| Â | Â | Precision mean/std | Recall mean/std | F-measure | Precision mean/std | Recall mean/std | F-measure | Precision mean/std | Recall mean/std | F-measure |
Duplications | PSE-HMM | 0.88/0.04 | 0.89/0.03 | 0.89 | 0.90/0.03 | 0.97/0.03 | 0.93 | 0.88/0.03 | 0.98/0.01 | 0.93 |
m-HMM | 1.00/0.00 | 0.71/0.1 | 0.83 | 1.00/0.00 | 0.76/0.04 | 0.86 | 1.00/0.00 | 0.75/0.03 | 0.86 | |
Pindel | 1.00/0.00 | 0.95/0.06 | 0.98 | 1.00/0.00 | 0.82/0.11 | 0.90 | 1.00/0.00 | 0.87/0.1 | 0.93 | |
CNV-seq | 0.99/0.01 | 0.53/0.06 | 0.69 | 0.99/0.00 | 0.53/0.02 | 0.69 | 0.99/0.00 | 0.59/0.09 | 0.74 | |
Delly | 1.00/0.00 | 1.00/0.00 | 1.00 | 1.00/0.00 | 1.00/0.00 | 1.00 | 1.00/0.00 | 1.00/0.00 | 1.00 | |
Deletions | PSE-HMM (heterozygous) | 0.68/0.10 | 1.00/0.01 | 0.81 | 0.35/0.10 | 1.00/0.00 | 0.52 | 0.70/0.08 | 1.00/0.03 | 0.82 |
PSE-HMM (homozygous) | 0.70/0.11 | 0.89/0.05 | 0.78 | 0.77/0.03 | 0.80/0.00 | 0.78 | 0.75/0.03 | 1.00/0.00 | 0.86 | |
PSE-HMM (hetero + homo)a | 0.69/0.02 | 0.96/0.02 | 0.80 | 0.64/0.02 | 1.00/0.02 | 0.78 | 0.72/0.02 | 1.00/0.02 | 0.84 | |
m-HMM (heterozygous) | 0.97/0.03 | 0.50/0.31 | 0.66 | 0.99/0.01 | 1.00/0.00 | 0.99 | 0.99/0.01 | 1.00/0.01 | 0.99 | |
m-HMM (homozygous) | 0.99/0.01 | 1.00/0.00 | 0.99 | 0.99/0.01 | 1.00/0.00 | 0.99 | 0.99/0.01 | 0.60/0.00 | 0.75 | |
m-HMM (hetero + homo)a | 0.98/0.01 | 0.67/0.03 | 0.79 | 0.99/0.01 | 1.00/0.02 | 0.99 | 0.99/0.01 | 0.78/0.01 | 0.87 | |
Pindel | 0.98/0.02 | 0.39/0.08 | 0.56 | 0.85/0.10 | 0.46/0.08 | 0.59 | 0.87/0.11 | 0.45/0.13 | 0.59 | |
CNV-seq | 0.98/0.00 | 0.92/0.04 | 0.95 | 0.98/0.00 | 0.96/0.01 | 0.97 | 0.98/0.00 | 0.96/0.02 | 0.97 | |
Delly | 0.99/0.01 | 0.47/0.11 | 0.64 | 0.99/0.00 | 0.51/0.04 | 0.68 | 0.99/0.01 | 0.45/0.12 | 0.62 | |