Table 1

Detection accuracy and computation time of four methods on simulated normal samples
CNV size CNV type PennCNV CBS Fused Lasso Group Fused Lasso
TPR FDR TPR FDR TPR FDR TPR FDR
5 Deletion 83.80 4.92 78.20 0.68 63.93 1.74 64.27 1.83
Duplication 58.53 4.67 11.67 10.26 20.00 37.76 39.87 14.33
10 Deletion 95.03 1.45 88.37 0.56 88.50 0.60 88.87 0.56
Duplication 93.43 0.78 56.50 4.40 83.90 12.60 91.60 3.85
20 Deletion 94.63 0.58 90.50 0.39 90.80 0.47 90.83 0.47
Duplication 96.13 0.92 86.22 3.58 92.77 4.95 94.98 2.13
30 Deletion 94.57 0.28 93.30 0.29 89.38 0.52 89.77 0.53
Duplication 96.09 0.05 90.77 1.61 94.32 1.78 94.98 1.29
40 Deletion 97.83 0.59 97.58 0.09 97.28 0.19 97.28 0.19
Duplication 94.61 0.46 92.77 0.98 93.94 1.15 94.63 0.75
50 Deletion 94.33 0.07 92.76 0.04 90.47 0.11 90.48 0.11
Duplication 94.50 0.09 93.81 0.74 93.11 0.79 93.64 0.49
 Overall Deletion 95.02 0.55 93.06 0.19 91.08 0.33 91.19 0.34
 Overall Duplication 93.82 0.44 86.92 1.55 90.56 2.85 92.46 1.38
 Overall 94.42 0.49 89.99 0.85 90.82 1.60 91.83 0.87
Time (sec.) 0.48 (0.01) 0.78 (0.69) 0.22 (0.13) 0.28 (0.05)

TPR and FDR are measured as the percentage of related SNPs. Overall accuracy is calculated by pooling all sequences with a given type of CNV. Also reported are the average and standard deviation of the number of seconds required for the analysis of one sequence.

Zhang et al.

Zhang et al. BMC Bioinformatics 2012 13:205   doi:10.1186/1471-2105-13-205

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