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ANNOVAR is a command line Perl program for genome annotation. It is used extensively by the scientific community, having been downloaded more than 30,000 times and cited in over 100 scientific publications. The efficient program enables annotation of a whole genome in less than four minutes and filtering of important variants in less than 15 minutes – all with minimal setup and full freedom to integrate the program into your variant annotation pipeline.




Flexible annotation options

Given a list of variants, ANNOVAR can perform:

  • Gene-based annotation, identifying whether a protein coding change has resulted using your gene definition system of choice
  • Region-based annotation, identifying affected genomic regions that lie outside protein-coding regions
  • Filter-based annotation, identifying known variants documented in public and licensed databases
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Ready-to-go annotation

ANNOVAR works with hundreds of pre-compiled, up-to-date annotation sources including all tracks from the UCSC Genome Browser. When HGMD is licensed with ANNOVAR, it provides comprehensive annotation for all published inherited disease mutations. Working with non-human genomes? ANNOVAR provides annotation for diverse species including mouse, fly, worm, yeast and many more.



Easy integration

As a command line Perl program, ANNOVAR can run as a standalone application on diverse hardware systems where standard Perl modules are installed. Configuration of the Perl source code enables easy integration into your own or third party variant annotation pipelines.

ANNOVAR runs on Linux, Mac and Windows systems with standard Perl modules installed.