VALOR2: characterization of large-scale structural variants using linked-reads

Table 1 Prediction performance evaluation using simulated structural variants

Variant	Tool	# Sim.	# Pred.	TP	FP	FN	Pr.	Rec.	F1
Duplications (direct)	VALOR2	111	103	89	14	22	0.86	0.80	0.83
Duplications (inverted)	VALOR2	49	51	43	8	6	0.84	0.88	0.86
Inversions	VALOR2	90	65	54	11	36	0.83	0.60	0.70
	VALOR₁	90	63	47	13	43	0.78	0.52	0.63
	LUMPY/smoove	90	35	27	7	63	0.79	0.30	0.44
	DELLY	90	358	39	293	51	0.12	0.43	0.18
	TARDIS	90	43	34	1	56	0.97	0.38	0.54
	Sniffles	90	787	72	603	18	0.11	0.80	0.19
	Long Ranger	90	75	54	20	36	0.73	0.60	0.66
	Long Ranger ∪ VALOR2 ^‡	90	102	70	31	20	0.69	0.78	0.73
	Long Ranger ∩ VALOR2	90	38	38	0	52	1.00	0.42	0.59
Deletions	VALOR2	85	81	74	7	11	0.91	0.87	0.89
	LUMPY/smoove	85	292	66	226	19	0.23	0.78	0.35
	DELLY	85	496	72	424	13	0.15	0.85	0.25
	TARDIS	85	152	70	82	15	0.46	0.82	0.59
	Sniffles	85	467	72	395	13	0.15	0.85	0.26
	Long Ranger	85	262	79	175	6	0.31	0.93	0.47
	Long Ranger ∪ VALOR2 ^‡	85	270	163	185	3	0.47	0.98	0.63
	Long Ranger ∩ VALOR2	85	84	79	5	6	0.94	0.93	0.93
Translocations	VALOR2	38	27	27	0	11	1.00	0.71	0.83
	LUMPY/smoove	38	4	2	2	36	0.50	0.05	0.10
	DELLY	38	116	30	86	8	0.26	0.79	0.39
	Long Ranger	38	29	26	3	12	0.90	0.68	0.78
	Long Ranger ∪ VALOR2 ^‡	38	38	53	3	3	0.95	0.95	0.95
	Long Ranger ∩ VALOR2	38	18	18	0	20	1.00	0.47	0.64

We evaluate the prediction performance of only large SVs (> 80 kbp for inversions, > 40 kbp for duplications, > 100 kbp for deletions, and > 100 kbp for translocations). Note that VALOR₁, LUMPY, DELLY, Sniffles, and Long Ranger are not able to call interspersed duplications, and TARDIS can call duplications < 10 kb, which is smaller than the variants shown in this table. Precision is calculated as \(\frac {\text {TP}}{\text {TP+FP}}\), and recall is defined as \(\frac {\text {TP}}{\text {TP+FN}}\), where TP is the true positive, FP is the false positive, FN is the false negative, Pr. is the precision, and Rec is the recall. F1-score (shown as F1) is calculated as \(2\times \frac {\text {precision}\times \text {recall}}{\text {precision + recall}}\). ^‡SV calls predicted by both Long Ranger and VALOR2 (> 50% reciprocal overlap) are merged into a single call. Best values are highlighted with boldface font

ISSN: 1474-760X