CLOVE: classification of genomic fusions into structural variation events

BMC Bioinformatics

Table 2 Results for SV recovery from the output of Socrates and Crest before (^R) and after (^C) classification with CLOVE in real sequencing data

Organism	Tool	Data	TP	HTP	FP	FN	Sn (95% CI)	Pr (95% CI)	Acc (95% CI)
Ecoli (SRX803011)	Socrates	M5^R	8	7	33	6	0.71 (.50,.86)	0.31 (.20,.45)	0.28 (.18,.40)
		M5^C	12	0	0	8	0.60 (.39,.78)	1.00 (.76,1.0)	0.60 (.39,.78)
		M0^R	8	13	49	0	1.00 (.85,1.0)	0.30 (.21,.42)	0.30 (.21,.42)
		M0^C	17	2	0	2	0.90 (.71,.97)	1.00 (.83,1.0)	0.90 (.71,.97)
	Crest	R	7	7	4	6	0.70 (.48,.85)	0.77 (.55,.91)	0.58 (.39,.76)
	Crest	C	10	0	0	10	0.50 (.30,.70)	1.00 (.72,1.0)	0.50 (.30,.70)
	Socrates + Crest	R	8	13	50	0	1.00 (.85,1.0)	0.30 (.20,.41)	0.30 (.20,.41)
	Socrates + Crest	C	17	3	0	1	0.95 (.77,1.0)	1.00 (.84,1.0)	0.95 (.77,1.0)
Human (NA12878)	Delly	R	1447	0	6818	1932	0.43 (.41,.44)	0.18 (.17,.18)	0.14 (.14.15)
	Delly	C	1437	0	0	1942	0.43 (.41,.44)	1.00 (1.0,1.0)	0.43 (.41,.44)
	Socrates	R	900	0	3781	2361	0.28 (.26,.29)	0.19 (.18,.20)	0.13 (.12.14)
	Socrates	C	894	0	0	2403	0.27 (.26,.29)	1.00 (1.0,1.0)	0.27 (.26,.29)
	Delly + Socrates	R	1819	0	10,394	1464	0.55 (.54,.57)	0.14 (.14,.16)	0.13 (.13,.14)
	Delly + Socrates	C	1816	0	0	1493	0.55 (.53,.57)	1.00 (1.0,1.0)	0.55 (.53,.57)

Columns refer to true positive events (TP), half true positives (HTP), false positives (FP), false negatives (FN), sensitivity/recall (Sn), precision (Pr), and accuracy (Acc). Confidence intervals calculated through binconf in R are supplied for the latter three columns

ISSN: 1471-2105