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ANNOVAR

An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). Using a desktop computer, ANNOVAR requires ∼4 min to perform gene-based annotation and ∼15 min to perform variants reduction on 4.7 million variants, making it practical to handle hundreds of human genomes in a day.

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1 user review

1 user review

Pierre-Julien VIAILLY's avatar image

Pierre-Julien VIAILLY

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.

ANNOVAR forum

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ANNOVAR classification

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

ANNOVAR specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
Perl
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
Yes

ANNOVAR distribution

versioning

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No versioning.

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ANNOVAR support

Maintainer

  • Kai Wang <>

Credits

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Publications

Institution(s)

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

Link to literature

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