Table 3.
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 | - | - | + | - | + | - | - | - | - | + |
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.