ExCNVSS: A Noise-Robust Method for Copy Number Variation Detection in Whole Exome Sequencing Data

Table 1

CNV detection performances across variant sizes using simulated data sets. Each method was run with its default parameters.

Size of variants	100~159 bp	160~299 bp	300~8260 bp
Number of simulated instances (gain/loss)	438 (212/226)	430 (219/211)	93 (52/41)
Size of gain instances (min/max)	Gain (120 bp/151 bp)	Gain (184 bp/296 bp)	Gain (305 bp/8260 bp)
Size of loss instances (min/max)	Loss (120 bp/151 bp)	Loss (178 bp/299 bp)	Loss (301 bp/1561 bp)
ExCNVSS
Number of correctly detected instances (gain/loss)	365 (164/201)	383 (192/191)	82 (45/37)
FNR/FPR (%)	16.7/2.7	10.9/2.2	12.1/6.3
Detected region size (bp)	Gain (120/151)	Gain (184/296)	Gain (305/8260)
(Min/max)	Loss (120/151)	Loss (178/299)	Loss (301/1561)
ExCNVSS_noRatio
Number of correctly detected instances (gain/loss)	294 (105/189)	332 (141/191)	56 (18/38)
FNR/FPR (%)	32.8/6.4	22.8/4.3	42.0/9.5
Detected region size (bp)	Gain (120/151)	Gain (184/296)	Gain (305/8260)
(Min/max)	Loss (120/151)	Loss (178/299)	Loss (301/1561)
Excavator
Number of correctly detected instances (gain/loss)	221 (100/121)	202 (94/108)	43 (26/17)
FNR/FPR (%)	50.3/0.1	53.4/0.1	52.8/0.8
Detected region size (bp)	Gain (120/151)	Gain (207/296)	Gain (305/871)
(Min/max)	Loss (120/151)	Loss (178/271)	Loss (359/603)
Contra
Number of correctly detected instances (gain/loss)	247 (147/100)	371 (182/189)	44 (35/9)
FNR/FPR (%)	42.7/0.2	13.1/0.0	51.7/0.0
Detected region size (bp)	Gain (120/151)	Gain (184/296)	Gain (305/8260)
(Min/max)	Loss (120/151)	Loss (196/299)	Loss (303/1561)
ExomeCNV
Number of correctly detected instances (gain/loss)	24 (24/0)	69 (69/0)	18 (17/1)
FNR/FPR (%)	94.3/0.0	84.3/0.0	78.8/0.0
Detected region size (bp)	Gain (120/151)	Gain (191/296)	Gain (305/8260)
(Min/max)	Loss ()	Loss ()	Loss (1561/1561)