Wednesday, August 31, 2011

Kaviar's webtool (and now also standalone) - filter out KNOWN variants

Kaviar's homepage: (~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?

Summary: 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.
=> KAVIAR can be used online and also as standalone collection of perl scripts related to either hg18 or hg19 reference genomes in order to preserve your data from internet exposure (please refer to the home page for links and info).

(Via Kaviar's homepage. please do not ask questions here, this page just reproducing some of the site content)