VAAST (Variant Annotation, Analysis, and Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds upon existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use fashion. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any existing methodology.
In: The American Journal of Human Genetics, 94 (4), pp. 599 - 610, 2014, ISSN: 0002-9297.
In: Current Protocols in Human Genetics, 2014.
In: Genetic Epidemiology, 2013.
A probabilistic disease-gene finder for personal genomes. Journal Article
In: Genome research, 21 (9), pp. 1529–1542, 2011, ISSN: 1549-5469.
In: American journal of human genetics, 89 (1), pp. 28–43, 2011, ISSN: 1537-6605.
- BioITWorld: VAAST potential for new genome mutation hunting software
- BoingBoing: Genomic research – faster, cheaper, more hope
- Children's Hospital of Philadelphia: Next generation gene sequencing brings personal genomics closer
- FierceBioTech IT: "VAAST" software could spot disease genes
- Forbes.com: A tragic case and a genomic hope
- Nature News: Software pinpoints cause of mystery genetic disorder
- Salt Lake Tribune: Utah researchers help find mutation that kills baby boys
- Science Daily: Next-generation gene sequencing brings personal genomics closer, IDs mutation in new syndrome
- Standard-Examiner: Ogden family grieving over 3 boys gets answers about genetic mutation
Licensing and Download
VAAST was developed as a collaboration between the Yandell Lab at the University of Utah and Omicia, Inc. of Emeryville, CA. The University of Utah freely licenses VAAST for academic research use. For commercial, clinical and all other uses, please contact Martin Reese of Omicia, Inc.
- VAAST Users Mailing List
To keep up to date on the release date. In the weeks leading up to publication, the VAAST software will be available for a limited release for beta testing. Please contact Mark Yandell if you would like to help with pre-release testing.
- GFF3 Specification
- GVF Specification
- 10Gen Personal Genomics Data Set