Table 3.
Rapid variant annotation tools
| Name | Description | URL |
|---|---|---|
| ANNOVAR | Efficient software tool to use up-to-date information to functionally annotate genetic variants detected from diverse genomes. | http://www.openbioinformatics.org/annovar/ |
| AnnTools | Comprehensive and versatile annotation toolkit for genomic variants. | http://anntools.sourceforge.net/ |
| dbNSFP | A lightweight database of human non-synonymous SNPs and their functional predictions. | https://sites.google.com/site/jpopgen/dbNSFP |
| EVA | An efficient and versatile tool for filtering strategies in medical genomics. | http://plateforme-genomique-irib.univ-rouen.fr/EVA/index.php |
| Exome Variant Server | Provides different calculated values (GERP, GRANTHAM, etc.) and annotations for SNPs. | http://evs.gs.washington.edu/EVS/ |
| gSearch | gSearch compares sequence variants in the Genome Variation Format (GVF) or VCF with a pre-compiled annotation or with variants in other genomes. | http://ml.ssu.ac.kr/gSearch/index.html |
| HugeSeq | A pipeline for detection and annotation of genetic variations. | http://hugeseq.snyderlab.org/ |
| MuSiC | Comprehensive mutational analysis pipeline to segregate passenger and driver mutations from cancer genomes. | http://gmt.genome.wustl.edu/genome-music/current/ |
| NGS-SNP | Collection of command-line scripts for providing rich annotations for SNPs. | http://stothard.afns.ualberta.ca/downloads/NGS-SNP/ |
| SeattleSeq Annotation | Provides annotation of known and novel SNPs. | http://snp.gs.washington.edu/SeattleSeqAnnotation/ |
| snpEff | Variant annotation and effect prediction tool. | http://snpeff.sourceforge.net/ |
| SVA | Software system designed for annotation and visualization of genetic variants. | http://www.svaproject.org/ |
| STORMSeq | Cloud computing solution for read mapping, read cleaning, and variant calling and annotation. | https://github.com/konradjk/stormseq |
| TREAT | Targeted RE-sequencing Annotation Tool. | http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm |
| VAAST | Probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. | http://www.yandell-lab.org/software/vaast.html |
| VARIANT | VARIANT (VARIant ANalysis Tool) can report the functional properties of any variant in all the human, mouse or rat genes. | http://variant.bioinfo.cipf.es/ |
| Variant Reporter | Generate a report of known variants and functional consequences. | www.ncbi.nlm.nih.gov/variation/tools/reporter |
| Variant Tools | Tool for the annotation, selection and analysis of variants in the context of next-gen sequencing analysis. | http://varianttools.sourceforge.net/ |