Tool | URL | Description | Features | Limitations |
---|---|---|---|---|
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 | 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 | 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 | 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 | 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 | 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 | 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 | A Java web application for variant annotation and visualization | Intuitive interface with integrated genome viewer | Highly specific requirement for internet browser; slow performance | |
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 | 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 | 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 |