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

BMC Bioinformatics

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

	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)

ISSN: 1471-2105