KAVIAR: an accessible system for testing SNV novelty.
- ISSN: 13674811
- DOI: 10.1093/bioinformatics/btr540
- PubMed: 21965822
Abstract
SUMMARY: With the rapidly expanding availability of data from personal genomes, exomes and transcriptomes, medical researchers will frequently need to test whether observed genomic variants are novel or known. This task requires downloading and handling large and diverse data sets from a variety of sources, and processing them with bioinformatics tools and pipelines. Alternatively, researchers can upload data to online tools, which may conflict with privacy requirements. We present here Kaviar, a tool that greatly simplifies the assessment of novel variants. Kaviar includes a) an integrated and growing database of genomic variation from diverse sources, including over 55 million variants from personal genomes, family genomes, transcriptomes, SNP databases and population surveys, and b) software for querying the database efficiently. AVAILABILITY: Kaviar is programmed in Perl and offered free of charge as Open Source Software. Kaviar may be used online, as a programmatic web service, or downloaded for local use, from http://db.systemsbiology.net/kaviar. The database is also provided. CONTACT: GustavoSystemsBiology.org.
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