Table 2.

Accuracy estimation of four call methods.

Sample		Genotype calls	†Sanger examined	TP (a)	FP (b)	FN (c)	Precision (a)/(a + b)	Recall (a)/(a + c)	F-measure
NA18943	IMSindel	60	54	49	5	14	0.91	0.78	0.84
	GATK	39	30	26	4	37	0.87	0.41	0.56
	PINDEL	70	60	32	28	31	0.53	0.51	0.52
	ScanIndel	32	24	20	4	43	0.83	0.32	0.46
NA18948	IMS	47	36	32	4	22	0.89	0.59	0.71
	GATK	17	15	15	0	39	1.00	0.28	0.43
	PINDEL	65	49	30	19	24	0.61	0.56	0.58
	ScanIndel	40	27	19	8	35	0.70	0.35	0.39
NA12878	IMSindel	17	—	16	1	8	0.94	0.67	0.78
	GATK	15	—	7	8	17	0.47	0.29	0.36
	PINDEL	22	—	14	8	10	0.64	0.58	0.61
	ScanIndel	19	—	10	9	14	0.53	0.42	0.47

^†The number of genotypes that could be examined using Sanger sequencing.