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ANNOVAR
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[http://www.openbioinformatics.org/annovar/]
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A software tool written in Perl to perform gene-based, region-based and filter-based annotation
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Rapid and up-to-date annotations for multiple species; thousands of annotation types are supported
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Requires format conversion for VCF files; command line interface cannot be accessed by many biologists
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AnnTools
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[http://anntools.sourceforge.net/]
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A software tool written in Python to annotate SNVs, indels and CNVs
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Fast information retrieval by MySQL database engine; output in VCF format for easy downstream processing
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Only supports human genome build 37; does not annotate variant effect on coding sequence
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Mu2a
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[http://code.google.com/p/mu2a/]
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A Java web application for variant annotation
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Web interface for users with limited bioinformatics expertise; output in Excel and text formats
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Does not allow annotation of indels or CNVs
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SeattleSeq
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[http://snp.gs.washington.edu/SeattleSeqAnnotation/]
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A web server that provides annotation on known and novel SNPs
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Multiple input formats are supported; users can customize annotation tasks
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Limited annotation on indels or CNVs
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Sequence Variant Analyzer
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[http://www.svaproject.org/]
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A graphical Java software tool to annotate, visualize and organize variants
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Intuitive graphical user interface; ability to prioritize candidate genes from multiple patients
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Functionality is not very customizable; depends on ENSEMBL database for annotations
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snpEff
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[http://snpeff.sourceforge.net]
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A command-line software tool to calculate the effects of variants on known genes such as amino acid changes
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Rapid annotation on multiple species and genome builds; supports multiple codon table
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Only supports gene-based annotation
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TREAT
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[http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm]
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A command-line software tool with rich integration of publicly available and in-house developed annotations
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An Amazon Cloud Image is available for users with limited bioinformatics infrastructure; offers a complete set of pipelines to process FASTQ files and generates annotation outputs
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Only supports ENSEMBL gene definition and with limited sets of annotations
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VAAST
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[http://www.yandell-lab.org/software/vaast.html]
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A command-line software tool implementing a probabilistic disease-gene finder to rank all genes
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Prioritize candidate genes for Mendelian and complex diseases
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Main focus is disease gene finding with limited set of annotations
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VARIANT
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[http://variant.bioinfo.cipf.es]
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A Java web application for variant annotation and visualization
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Intuitive interface with integrated genome viewer
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Highly specific requirement for internet browser; slow performance
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VarSifter
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[http://research.nhgri.nih.gov/software/VarSifter/]
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A graphical Java program to display, sort, filter and sift variation data
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Nice graphical user interface; allows interaction with Integrative Genomics Viewer
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Main focus is variant filtering and visualization with limited functionality in variant annotation
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VAT
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[http://vat.gersteinlab.org/]
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A web application to annotate a list of variants with respect to genes or user-specified intervals
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Application can also be deployed locally; can generate image for genes to visualize variant effects
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Requires multiple other packages to work; only supports gene-based annotation by GENCODE
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wANNOVAR
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[http://wannovar.usc.edu/]
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A web server to annotate user-supplied list of whole genome or whole exome variants with a set of pre-defined annotation tasks
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Easy-to-use interface for users with limited bioinformatics skills
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Limited set of annotation types are available
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