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Table 4 Illumina-only method comparison

From: Assessing structural variation in a personal genome—towards a human reference diploid genome

Program Total called Supported Unsupported FDR Sensitivity
CNVnator 6,197 1,211 4,986 80.46% 22.62%
BreakDancer 5,520 2,269 3,251 58.89% 42.39%
Delly 3,720 1,669 2,051 55.13% 31.18%
Crest 2,219 1,889 330 14.87% 35.29%
Pindel 4,451 3,035 1,416 31.81% 56.70%
SV-STAT 892 876 16 1.79% 16.36%
Tiresias 1,347 417 930 69.04% 7.79%
Spiral 1,881 1,824 57 3.03% 34.07%
Parliament 3,082 2,852 258 8.37% 57.34%
  1. Performance for each Illumina-only method is summarized. Supported and Unsupported columns indicate the number of calls with and without local hybrid assembly support, respectively. False discovery rate (FDR) and sensitivity are calculated using all 17,704 Illumina Only reference inconsistent loci and the subset of 5,584 that are supported by hybrid assembly.