< Kaviar > (~Known VARiants) is a very simple tool for answering a very specific question:
What variants have been reported already for a given specific genomic location?
Importance

  • Genome and transcriptome sequencing reveal each individual's unique pattern of genomic variations. A fraction of the personal variants observed via sequencing are false positive artifacts of random sequencing error, which may confound the search for disease-causing mutations. When family genomes are available, over half of the errors may be identified by inheritance state analysis. Variants frequently observed in other personal genomes are less likely to be artifacts.
  • Kaviar is a compilation of SNVs observed in humans, designed to facilitate testing for the novelty and frequency of SNVs. The web interface is convenient for testing small to medium-sized sets of SNVs. For high-throughput filtering of variants observed in personal genomes, we recommend using the web service interface, or downloading the database and tools for running locally.
  • In any case, caution should be used when interpreting results, as SNV novelty need not imply functional or clinical relevance. Conversely, known SNVs may have unknown functional implications. In some cases, even the reference form may actually be the detrimental variant.
Information

  • Kaviar currently lists 53 million variant sites.
  • Last data update: November 21st, 2011. (Use developmental version, below, for more recent data.)
  • See the full list of data sources that have been incorporated into Kaviar.
  • Read the changelog.
Using it online

  • Query Kaviar's database interactively.
    This is the Kaviar server at the Institute for Systems Biology.
    Using this server is the simplest option if your data are not restricted (by IRB protocols or other constraints) in such a way that you cannot use web services for analysis.
  • Query Kaviar as a web service
    You can use our server as a web service using this URL in your code.
    We provide some example code.
    Please note: the same privacy considerations as above still apply.
Using it locally

  • Download the code and database (version 111121):
Developmental version
Communication

  • Questions, comments, bug reports, and suggestions for improvements or additional data sets are most welcome!
  • Would you like to receive notification of updates to Kaviar? Follow via Twitter, or join the Kaviar-announce google group.
  • If you find Kaviar useful for your work, please cite:
    Glusman G, Caballero J, Mauldin DE, Hood L and Roach J (2011) KAVIAR: an accessible system for testing SNV novelty. Bioinformatics, doi: 10.1093/bioinformatics/btr540.