Table 3.

Performance of eight low-frequency variant callers on the reference datasets N0015 and N13532.

Dataset	Tool	No. of calls a	No. of variants b	True positive	False positive	Sensitivity (%)	Precision (%)	F1-score	Accuracy (%)
N0015 (VAF ≈ 5%)	DeepSNVMiner	499	338	328	171	97.04	65.73	0.78	99.37
	MAGERI	1351	338	326	1025	96.45	24.13	0.39	96.37
	smCounter2	516	338	338	178	100	65.5	0.79	99.38
	UMI-VarCal	810	338	325	485	96.15	40.12	0.57	98.26
	SiNVICT	506	338	326	180	96.45	64.43	0.77	99.33
	outLyzer	411	338	274	137	81.07	66.67	0.73	99.30
	Pisces	590	338	338	252	100	57.29	0.73	99.18
	LoFreq	608	338	332	276	98.22	54.61	0.7	99.04
N13532 (VAF ≈ 0.5%)	DeepSNVMiner	31	17	15	16	88.24	48.39	0.62	99.94
	MAGERI	271	17	12	259	70.59	4.43	0.08	99.13
	smCounter2	31	17	17	14	100	54.84	0.71	99.95
	UMI-VarCal	92	17	17	75	100	18.48	0.31	99.75
	SiNVICT	23	17	1	22	5.88	4.35	0.05	99.87
	outLyzer	12	17	1	11	5.88	8.33	0.07	99.91
	Pisces	23	17	1	22	5.88	4.35	0.05	99.97
	LoFreq	752	17	14	738	82.35	1.86	0.04	97.56

The variant allele frequencies of N0015 and N13532 were around 5% and 0.5%, respectively.

^anumber of calls, ^bnumber of variants.