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Comparison to AVIA

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Analysis of Genomic Variations with AVIA

Comparision of AVIA to other Annotation Tools

A cursory comparison of various annotation web servers was performed and results are included below (Note: these websites may have updated since the time of this comparison in Jan 2014). SNPEff is grayed out because there is no web server available; however it is included in the comparison because it is easily integrated with Galaxy.
  AVIAv2.0 AVIAv1.0 wANNOVAR** VARIANT** CRAVAT Variant Effect Predictor SeattleSeq Annotation SNP Nexus SNPEff Protein Variant Scoring Algorithms
MutationTaster MutationAssessor SIFT Polyphen2 SNAP
Using the ANNOVAR framework, AVIA is a fast, intuitive server that annotates many aspects of the variants, including functional consequence, scoring algorithms, and SNP assessment. It is also easily expandable to add other annotations and customizable to user's specifications. wANNOVAR is the web-based tool that runs ANNOVAR, a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data. VARIANT (VARIant ANalysis Tool) can report the functional properties of any variant in all the human, mouse or rat genes and the corresponding neighborhoods. Also other non-coding extra-genic regions, such as miRNAs are included in the analysis. CRAVAT (Cancer-Related Analysis of VAriants Tookit) a web-based application that provides a simple interface to prioritize genes and variants important for tumoigenesis in a single step. The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. The SeattleSeq Annotation server provides annotation of SNVs (single-nucleotide variations) and indels, both known and novel. SNPnexus was designed to simplify and assist in the selection of functionally relevant Single Nucleotide Polymorphisms (SNP) for large-scale genotyping studies of multifactorial disorders. Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). MutationTaster evaluates disease-causing potential of sequence alterations The server predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. SIFT predicts whether an amino acid substitution affects protein function. SIFT prediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related sequences, collected through PSI-BLAST. PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. SNAP is a method for evaluating effects of single amino acid substitutions on protein function.
X X X X X X X X X X X X X
X X X X X
genomic, HGVS, gene lists, gene variant positions genomic, HGVS genomic genomic genomic genomic genomic genomic genomic cDNA positions, genomic, or HGVS genomic, protein genomic protein or dbSNP identifiers, protein sequence or protein position protein sequence and position
SIFT, PP2, MT, MA, Provean, FunSeq, VEST, CADD, FATHAMM SIFT, PP2, MT, MA SIFT,PP2, MT** VEST, MuPit (maps genomic coordinates to protein structures) SIFT, PP2 PP2 SIFT, PP2 MT MA SIFT PP2 SNAP
Filter normal vs tumor mutations (multi-column VCF file) X X Cancer analysis
X X X X (TFBS, CpG) X
40+ 20+ 17+** dbSNP, lincRNA, miRNA target site, TF binding site, CpG island, etc VEST, Empirical p-value, dbSNP, 1000G & ESP allele frequencies, Pubmed, GeneCards dbSNP, SIFT, PP2 17+ 11+ dbNSFP, GWAS, SIFT
both both Ensembl RefSeq both RefSeq both Ensembl Ensembl
all isoforms (by default) default no all isoforms ? all isoforms primary transcript with linkout N/A
X **
Circos Plots, summary plots, genome browser, jsmol protein structure (limited), PathView, Reference Expression by tissue, protein features Circos Plots, summary plots, genome browser graphs, summaries, IGV
VCF file, BED files, HGVS VCF file, BED files, HGVS VCF file BED-like files VCF file, BED files, MAQ formatted files, GFF files, CASAVA , custom, GATK formatted files BED HGVS N/A
gene lists, protein coding mutations (HGVS) N/A
Yes No, but integrated IGV viewer and gene ontology Yes, links available for Pubmed articles from Excel Yes Yes
miRNA, FunSeq2 miRNA
by Gene, filter by cutoffs or consequence, and on web interface, using javascript by Gene, filter by cutoffs Filter by cutoffs by region, gene, or by consequence type Gene by default Allele frequences X
X X X
GNF, NetPath
X using bioDBnet
one aggregated report file, multiple text files, multiple image files including KEGG pathways, vcf file(if user input was VCF) one aggregated report file, multiple images for Circos, genelist text multiple text by consequence type text text text text , graphs text text text text text text
*Abbreviations: Polyphen2(PP2), Mutation Taster(MT), Mutation Assessor (MA), Combined Annotation Dependent Depletion (CADD), Variant Effect Scoring Tool (VEST)
**more available on command line interface


The following annotation tools have not been included in the table because they do not have web servers:
  • ANNOVAR (UNIX based CLI)
  • SNP eff (java based desktop application)
  • Variant Annotation Tool (VAT) (UNIX based CLI)
  • VariantAnnotator (available through GATK)
  • Sequence Variant Analyzer ( SVA) (available as a desktop application)
  • VAAST
  • Gemini (GEnome MINIng) (UNIX based CLI)
Click here to view great comparison of various annotation tools.

***If you are one of the developers for one of these tools and see some errors, please contact us using our web form by clicking here.