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Table 1 Summary of annotations available in VariantDB

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

Source tool

Available annotations

Reference

GATK genotypers

Variant coverage, allelic ratio, genotype, Phred polymorphism, Phred genotype, quality by depth, mapping quality, ranksums, strand bias

[16]

ANNOVAR

Allele frequencies (1KG/ESP/dbSNP), pathogenicity (dbNSFP, CADD, GERP++), segdups, genes (symbol, exon, location, effect; UCSC/RefGene/Ensembl)

[28]

SnpEff

Variant effect, effect impact, location, protein change, gene (Ensembl)

[25]

Web tools

MutationTaster, SIFT, PROVEAN, Grantham

[37]-[39]

Gene Ontology

Associated Gene Ontology IDs, terms, and term types. First level parental terms

[40]

ClinVar

Link to ClinVar, variant type, pathogenic class, class comment, affected gene and transcript, latest update, associated disease, links to external data sources, publications

[41]

Gene panels

Affected gene, comments, panel name

Â