< Kaviar3 > 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, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants. The web interface is convenient for testing small to medium-sized sets of variant positions. For high-throughput filtering of variants observed in personal genomes, we recommend using the web service interface, or downloading the VCF files for analysis locally.
  • In any case, caution should be used when interpreting results, as variant novelty need not imply functional or clinical relevance. Conversely, known variants may have unknown functional implications. In some cases, even the reference form may actually be the detrimental variant.
Information

  • Kaviar currently lists 151 million SNV (single nucleotide variant) sites
  • Kaviar currently incorporates data from 31 projects encompassing nearly 72,000 individuals (8.4K whole genome, 63.5K exome). View a treemap depiction. Auxiliary info available for some data sources.
  • Kaviar also contains 27 million indels and complex variants from a subset of the data sources.
  • Kaviar excludes cancer genomes but includes some data from cell lines and individuals affected by disease.
  • An effort was made to exclude data from related individuals.
  • Last update: January 14, 2015 (version 141127)
  • Read the changelog and the list of known issues.
Using it online
Using it locally

  • Download a 1.9 GB VCF file containing allele frequencies for all variants in Kaviar for GRCh37 (hg19)
  • Browse other available VCF downloads containing data source annotations, omitting very rare variants (compact), and/or for other versions of the reference genome.
Communication