VariantDB: a flexible annotation and filtering portal for next generation sequencing data

Table 3 Functional comparison of VariantDB with publicly available alternatives

	KggSeq	VariantMaster	BIERapp	AnsNGS	WEP	FamANN	PriVar	EVA	Annotate-it	VariantDB
Citation	[59]	[60]	[61]	[62]	[32]	[23]	[30]	[31]	[29]
Data management
Online	-	-	+	+	+	-	-	+	+	+
Collaborative projects	-	-	-	-	+	-	-	+	+	+
Inter-sample relations^a	+	+	+	-	+	+	+	+	+	+
Gene annotations
RefSeq annotations	+	+	+	+	+	+	+	+	+	+
Ensembl annotations	-	+	+	-	-	+	-	-	+	+
In silico gene panels	-	-	+	-	-	-	+	-	+	+
Population frequencies
Public (ESP, 1KG, dbSNP)	+	+	+	-	+	+	+	+	+	+
In-house samples^b	+	-	-	-	-	-	-	-	-	+
Pathogenicity predictions
dbNSFP^(c)	+	-	+	-	+	+	+	-	+	+
CADD	-	-	-	-	-	-	-	-	-	+
PROVEAN	-	-	-	-	-	-	-	-	-	+
Clincal
Disease information source	GSEA	-	ClinVar	MIM	-	-	HuGe	-	MIM	ClinVar
System implementation
Annotation updates^d	A	M	A	.	.	M	M	M	A	A
Retrospective updates	-	-	-	-	.	-	-	-	-	+
Upstream integration^e	-	-	-	-	+	+	-	-	-	+
Alignment visualization	-	-	+	-	+	-	-	-	-	+

^aRelations might be either specified at sample level or provided as pedigree files upon runtime. ^bUser-accessible sample genotypes are used to calculate a private set of MAFs. ^cBoth full and partial dbNSFP annotations are considered here. ^dA, automatic; M, manual annotation updates; or not specified (period). ^eDirect integration with genotyping tools or modules.

ISSN: 1756-994X