A study on fast calling variants from next-generation sequencing data using decision tree

BMC Bioinformatics

Table 4 Comparison of four variant callers for calling rare variants

AF		benchmark (high-conf)	Fuwa	Platypus	GATK-UG	GATK-HC	SAMtools
≤5%	count	282,869	207,098	201,577	210,190	209,119	207,187
≤5%	ratio (%)	–	73.21	71.26	74.31	73.93	73.24
≤1%	count	128,661	80,895	78,908	81,758	81,417	80,956
≤1%	ratio (%)	–	62.87	61.33	63.55	63.28	62.92
≤0.5%	count	92,309	55,630	54,280	56,137	55,928	55,646
≤0.5%	ratio (%)	–	60.26	58.80	60.81	60.59	60.28
≤0.1%	count	37,563	23,695	23,112	23,863	23,795	23,688
≤0.1%	ratio (%)	–	63.08	61.53	63.53	63.35	63.06

ISSN: 1471-2105