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 | |
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 |