In conclusion, ANNOVAR is a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data. Additionally, ANNOVAR provides flexible variants reduction pipeline that helps pinpoint a specific subset of variants most likely to be causal for diseases or traits. With the rapid development and deployment of next-generation sequencing technologies, we expect that ANNOVAR will facilitate taking full advantage of the upcoming massive amounts of sequencing data to expedite scientific discoveries.