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:
- VAT The Variant Annotation Tool calculates a rich set of annotations on the effects that variants have on genomic features based on terms described and constrained by the Sequence Ontology. These effects, like synonymous and missense changes, stop-gain and loss, splice site variants and others that provide additional information about the functional effect of a variant, which VAAST 2 uses to score features.
- VST The Variant Selection Tool performs set operations (intersection, union, complement, and difference) on a group of annotated GVF files to produce a merged representation of the group's variants in a CDR file. VST can be used to simply create a merged set of variants for the target or background genomes required as input to VAAST 2, but can also manufacture arbitrarily complex selections based on nested set operations.
- VAAST 2 A probabilistic search tool that uses the outputs of VAT and VST to identify damaged genes and their disease-causing variants in personal genome sequences.
Is it ever going to be available for download? Even VAAST1 never had a download link. The Download link just goes to some kind of license fax form.
karl.stamm VAAST and VAAST2 are free for academic use. The licensing is required to prevent "for profit" institutions from using the code without permission. Fill out the form and you will get the VAAST download.
I think that the process of licensing via email and sending signed PDFs back and forth greatly reduces the number of people that would legitimately use the program and hence greatly impacts the acceptance of the tool. And thus indirectly it reduces the market awareness and potential for commercialization. It is only hurting the tool and the benefits are all imaginary.
Simply stating on the home page and in the licensing of the code that: This code is licensed for academic purposes only. For a commercial license you must contact us.
I have seen how many life sciences companies work. Those that have any value as potential clients are all EXTREMELY cautious about licensing and would never use a tool without a proper license. If anything they are overly cautious. It is difficult to impossible to hide what tool they used, and they have to disclose that when publishing, FDA reviews etc and the consequences that they would incur for breaking the licensing would be far more damaging to them.
Istvan Albert I will pass this sentiment along.
I have a licence for VAAST. Do I need to re-apply for VAAST2?
If you have access to the SVN version you should just be able to update it and you'll be using VAAST2. If not, message me and I'll get you access on your old license.
Hi Zev, Where I can download pre-annotated loss-of-function SNVs?