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Table 6 PSE-HMM is compared to other tools in detecting genome-wide deletions and tandem duplications of size 1 kb, 3 kb, and 5 kb

From: PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities

  CNV length
1 kb 3 kb 5 kb
   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
  1. The average and standard deviation of the precision (recall) values are calculated based on five different repeats of the whole simulation study with 10× sequencing coverage
  2. a hetero + homo stands for copy loss
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