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Table 2 A list of open-access bioinformatics software tools or web servers that can perform batch annotation of genetic variants from whole-exome/genome sequencing data*

From: Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress

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