Kaviar: An Accessible System for Testing SNV Novelty

Bioinformatics. 2011 Nov 15;27(22):3216-7. doi: 10.1093/bioinformatics/btr540. Epub 2011 Sep 28.

Abstract

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 datasets 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: (i) an integrated and growing database of genomic variation from diverse sources, including over 55 million variants from personal genomes, family genomes, transcriptomes, SNV databases and population surveys; and (ii) software for querying the database efficiently.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Nucleic Acid
  • Genetic Variation*
  • Genomics
  • Humans
  • Software*
  • Transcriptome