Identification of copy number variants from exome sequence data

Table 3 True positive (TP), false positive (FP) and TP/FP ratio for short CNVs (1–4 exons)

Program	1000 genomes exomes			Primary immunodeficiency patients
	TP	FP	TP/FP ratio	TP	FP	TP/FP ratio
CONIFER	0	0		4	6	0.67
XHMM	0	4		7	32	0.22
ExomeDepth	0	2		50	301	0.17
ExomeCopy	914	6591	0.14	161	1076	0.15
ExCopyDepth	63	267	0.24	52	669	0.08
Intersection of ExomeCopy/ExCopyDepth	34	76	0.45	44	478	0.09

TP, True positive CNVs (CNVs identified both exaCGH and computational programs); FP, False positive CNVs (CNVs identified only by computational programs but not by exaCGH); TP/FP ratio, Ratio between true positive and false positive CNVs.