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

BMC Systems Biology

Table 4 Somatic SNV calling performance comparison

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

ISSN: 1752-0509