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Table 4 Somatic SNV calling performance comparison

From: SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations

Metric Error SNVSniffer(M1) SomaticSniper VarScan2 JSM2 MuTect
Recall 1.0 % 94.86 86.62 77.43 91.26 93.47
  1.5 % 94.49 86.62 80.67 91.24 93.47
  2.0 % 94.00 86.62 80.50 91.23 93.47
Precision 1.0 % 95.87 99.77 95.02 99.68 84.76
  1.5 % 95.86 99.77 95.29 99.68 84.76
  2.0 % 95.85 99.78 95.36 99.68 84.76
F-score 1.0 % 95.36 92.73 85.33 95.28 88.90
  1.5 % 95.17 92.73 87.37 95.27 88.90
  2.0 % 94.92 92.74 87.30 95.27 88.90
Time(s) 1.0 % 275 183 1828 1364 3677
  1.5 % 273 180 1947 1361 3644
  2.0 % 271 179 1990 1368 3658
  1. Best results are highlighted in boldface