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Table 3 Functional comparison of VariantDB with publicly available alternatives

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

  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 relationsa + + + - + + + + + +
Gene annotations           
RefSeq annotations + + + + + + + + + +
Ensembl annotations - + + - - + - - + +
In silico gene panels - - + - - - + - + +
Population frequencies           
Public (ESP, 1KG, dbSNP) + + + - + + + + + +
In-house samplesb + - - - - - - - - +
Pathogenicity predictions           
dbNSFP(c) + - + - + + + - + +
CADD - - - - - - - - - +
PROVEAN - - - - - - - - - +
Clincal           
Disease information source GSEA - ClinVar MIM - - HuGe - MIM ClinVar
System implementation           
Annotation updatesd A M A . . M M M A A
Retrospective updates - - - - . - - - - +
Upstream integratione - - - - + + - - - +
Alignment visualization - - + - + - - - - +
  1. 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.