Comparative assessments of indel annotations in healthy and cancer genomes with next-generation sequencing data

BMC Medical Genomics

Table 5 Top 3 indel annotation program combinations (2 programs and 3 programs)

F rank	Combination of 2 tools	TP	FP	Recall	Precision	F
1	GATK_UG + GATK_HC	822,516	1,107,610	0.65	0.43	0.51
2	GATK_UG + Dindel	839,132	1,226,226	0.66	0.41	0.50
3	GATK_HC + Platypus	871,596	1,403,334	0.68	0.38	0.49

F rank	Combination of 3 tools	TP	FP	Recall	Precision	F
1	GATK_UG + GATK_HC + Dindel	804,060	978,793	0.63	0.45	0.53
2	GATK_UG + GATK_HC + SAMTools	725,419	768,246	0.57	0.49	0.52
3	GATK_UG + GATK_HC + Platypus	778,439	991,540	0.61	0.44	0.51

ISSN: 1755-8794