ANNOVAR specifications

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  • Animals
    • Caenorhabditis elegans
    • Drosophila melanogaster
    • Homo sapiens
    • Mus musculus
  • Fungi
    • Saccharomyces cerevisiae


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ANNOVAR distribution


ANNOVAR support


  • Kai Wang <>


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Center for Applied Genomics, Children’s Hospital of Philadelphia, Department of Biostatistics and Epidemiology and Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA

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Pierre-Julien VIAILLY's avatar image

Pierre-Julien VIAILLY

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ANNOVAR is a very useful Perl package for the annotation of genetic variants detected using NGS. Users can annotate VCF files (or other compatible formats) throw 3 modules :
- Gene-based annotations : identify wether SNPs or CNVs cause protein coding changes using RefSeq, UCSC, ENSEMBL, GENCODE or AceView. Example : “Giving a list of variants in VCF format, what are the genes impacted ?”
- Region-based annotations : identify variants in a specific genomic region. Example : “Giving a list of differentially methylated regions, what are the genes in these loci ?”
- Filter-based annotations : identify variants that are reported in specific databases such as dbNSFP (pathogenicity prediction algorithms), dbSNP, 1000 genomes, ClinVar or COSMIC. Custom databases can be created in GFF format. Example : “Giving a list of variants, how can I find those previously reported as cancer-relevant mutations ?”

Giving a list of VCFs, ANNOVAR produces tab-separated values files which can be easily integrated in bioinformatics pipelines or directly read in a spreadsheet.