Identification of copy number variants from exome sequence data

BMC Genomics

Table 2 True positive (TP)/false positive (FP) CNV ratio predicted from each program

Program	AvgTP	TP/FP ratio	Total CNV count³	Average CNVs per sample⁴
CoNIFER	1.33 (1.33)¹	0.92 (1.09)²	23	2.56
ExCopyDepth	28.11 (15.86)¹	0.34 (0.51)²	422	46.89
ExomeCopy	289.33 (226.0)¹	0.20 (0.21)²	11978	1330.89
ExomeDepth	1.11 (0.78)¹	0.67 (0.70)²	17	1.89
Intersection of ExomeCopy / ExCopyDepth	12.89 (7.33)¹	0.28 (0.33)²	218	24.22
XHMM	4.44 (3.56)¹	0.32 (0.53)²	92	10.22
CONTRA	17.88 (16.56)¹	0.20 (0.20)²	896	99.56

TP/FP ratio for each program was calculated using CNVs identified from 9, 1000 genomes samples run in both computational programs and exaCGH; Average true positive (AvgTP) = TP/9; TP/FP ratio = TP CNV count /FP CNV count; Average CNVs per sample = Total CNV count/9.
¹Average true positive calculated by excluding CNVs in X and Y Chromosomes.
²TP/FP ratio calculated by excluding CNVs in X and Y Chromosomes.
³Total number of CNVs predicted by each program excluding CNVs in X and Y Chromosomes (CNV counts for each program including X and Y Chromosomes are presented in Figure 1b).
⁴Average CNVs per sample calculated from counts presented in total CNV count column in Table 2.

ISSN: 1471-2164