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Table 1 Sensitivity and proxy positive predictive value (pPPV) summarized for each caller at varying depths. The pPPV values are shown in parenthesis

From: Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach

  Simulation 1 Simulation 2 Simulation 3 Mean SE
PBVI-OG      
150× 0.46 (0.90) 0.44 (0.88) 0.45 (0.88) 0.45 (0.89) 0.01 (0.01)
300× 0.71 (0.92) 0.72 (0.92) 0.70 (0.93) 0.71 (0.92) 0.01 (0.00)
600× 0.87 (0.91) 0.85 (0.88) 0.89 (0.92) 0.87 (0.90)_ 0.01 (0.01)
1200× 0.96 (0.88) 0.96 (0.80) 0.98 (0.78) 0.97 (0.82) 0.01 (0.03)
LoFreq      
150× 0.55 (0.82) 0.36 (0.76) 0.31 (0.79) 0.41 (0.79) 0.07 (0.02)
300× 0.74 (0.87) 0.55 (0.83) 0.46 (0.85) 0.58 (0.85) 0.08 (0.01)
600× 0.84 (0.89) 0.71 (0.86) 0.60 (0.88) 0.71 (0.87) 0.07 (0.01)
1200× 0.93 (0.87) 0.77 (0.87) 0.67 (0.89) 0.79 (0.87) 0.08 (0.01)
VarDict      
150× 0.89 (0.45) 0.82 (0.40) 0.84 (0.39) 0.84 (0.42) 0.02 (0.02)
300× 0.90 (0.77) 0.86 (0.71) 0.86 (0.73) 0.87 (0.74) 0.01 (0.02)
600× 0.87 (0.87) 0.85 (0.83) 0.83 (0.87) 0.85 (0.86) 0.01 (0.01)
1200× 0.87 (0.87) 0.85 (0.83) 0.83 (0.87) 0.85 (0.86) 0.01 (0.01)