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Table 2 Performance of smCounter, MuTect, and VarDict in detecting 1% variants in the coding region of N0030. Cutoffs were selected to represent optimal performance

From: Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller

Variant type Variant Caller TP FP FN TPR(%) FP /Mb PPV(%)
SNV smCounter 205 7 18 91.9 10 96.7
  MuTect 214 58 9 96.0 85 78.7
  VarDict 204 169 19 91.5 248 54.7
INDEL smCounter 45 5 4 91.8 7 90.0
  VarDict 43 100 6 87.8 147 30.1