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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