Variant Annotation, Analysis and Search Tool - VAAST 2

VAAST 2 (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST 2 builds upon existing phylogenetic conservation, amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of all 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 2 can score both coding (SNV, indel and splice site) and non-coding variants (SNV), evaluating the cumulative impact of both types of variants simultaneously. VAAST 2 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 2 thus has a much greater scope of use than any existing methodology.

The VAAST 2 package consists of three primary tools:

Note that another tool with the name VAT and similar functionality to VAAST's VAT was published recently by the Gerstein lab. You can access the Gerstein lab VAT on their web-site, however it's output is not compatible with VAAST 2.

Publications

Shirley MD Tang H Gallione CJ Baugher JD Frelin LP Cohen B North PE Marchuk DA Comi AM Pevsner J
N Engl J Med. 2013 May 23;368(21):1971-9.
Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, Huff CD, Hu H, Vickrey AI, Nielsen SCA, Stringham SA, Hu H, Willerslev E, Gilbert MTP, Yandell M, Zhang G, Wang J.
Science. 2013 Mar 1;339(6123):1063-7
Yandell M Huff CD Hu H Singleton M Moore B Xing J Jorde L Reese MG
Genome Res. 2011 Jul
Rope AF Wang K Evjenth R Xing J Johnston JJ Swensen JJ Johnson WJ Moore B Huff CD Bird LM Carey JC Opitz JM Stevens CA Jiang T Schank C Fain HD Robison R Dalley B Chin S South ST Pysher TJ Jorde LB Hakonarson H Lillehaug JR Biesecker LG Yandell M Arnesen T Lyon GJ
Am J Hum Genet. 2011 Jul 15;89(1):28-43

Press

License & Downloads

VAAST 2 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 2 for academic research use. For commercial, clinical and all other uses please contact Martin Reese at Omicia, Inc.

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