BMC Medical Genomics

Table 3 Pair-wise comparison between general indel calling programs

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

Recall	Varscan	GATK_UG	GATK_HC	Pindel	Dindel	Platypus	SAMTools
Precision
Varscan	–	0.40	0.41	0.30	0.41	0.39	0.36
GATK_UG	0.57	-	0.65	0.33	0.66	0.64	0.60
GATK_HC	0.59	0.43	–	0.34	0.72	0.68	0.65
Pindel	0.62	0.59	0.57	–	0.34	0.33	0.31
Dindel	0.58	0.41	0.38	0.56	–	0.70	0.68
Platypus	0.57	0.34	0.38	0.59	0.35	–	0.66
SAMTools	0.55	0.40	0.40	0.60	0.27	0.29	–

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ISSN: 1755-8794

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