Table 3.

Positive predictive value and sensitivity in case of GATK, Platypus, VarScan, LoFreq, FreeBayes, SNVer, SAMtools, VarDict, the combined output of all tools (eight tools), single-appreci8 and appreci8 in test sets 1–5

Approach	Test set 1		Test set 2		Test set 3		Test set 4		Test set 5
	Sens	PPV	Sens	PPV	Sens	PPV	Sens	PPV	Sens	PPV
GATK	0.92	0.82	0.90	0.73	0.95	0.31	0.86	0.73	0.92	0.94
Platypus	0.93	0.81	0.93	0.83	0.97	0.13	0.91	0.30	0.90	0.94
VarScan	0.84	0.84	0.82	0.73	0.91	0.51	0.73	0.55	0.71	0.94
LoFreq	0.98	0.29	0.98	0.71	0.94	0.31	0.73	0.01	0.79	0.88
FreeBayes	0.99	0.02	1.00	0.01	0.99	0.07	0.95	0.01	0.96	0.25
SNVer	0.91	0.91	0.94	0.81	0.97	0.10	0.64	0.04	0.73	0.98
SAMtools	0.82	0.83	0.81	0.75	0.93	0.68	0.70	0.53	0.86	0.99
VarDict	0.96	0.78	0.99	0.30	0.99	0.25	0.91	0.09	0.97	0.83
8 tools	1.00	0.02	1.00	0.01	0.99	0.05	0.99	0.01	1.00	0.25
single-appreci8	0.99	0.88	1.00	0.76	0.99	0.36	0.93	0.19	0.96	0.97
appreci8	0.98	0.99	1.00	0.99	0.99	0.76	0.93	0.65	1.00	1.00