Tool: Vat - Variant Annotation Tool - Functional Variant Annotation Of Personal Genomes
gravatar for Malachi Griffith
8.3 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

Variant Annotation Tool

A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.

The functional annotation of variants obtained through sequencing projects is generally assumed to be a simple intersection of genomic coordinates with genomic features. However, complexities arise for several reasons, including the differential effects of a variant on alternatively spliced transcripts, as well as the difficulty in assessing the impact of small insertions/deletions and large structural variants. Taking these factors into consideration, we developed the Variant Annotation Tool (VAT) to functionally annotate variants from multiple personal genomes at the transcript level, as well as obtain summary statistics across genes and individuals. VAT also allows visualization of the effects of different variants, integrates allele frequencies and genotype data from the underlying individuals, and facilitates comparative analysis between different groups of individuals. VAT can either be run through a command-line interface or as a web application. Finally, in order to enable on-demand access, and to minimize unnecessary transfers of large data files, VAT can be run as a virtual machine in a cloud-computing environment.Availability and implementation: VAT is implemented in C and PHP. The VAT web-service, Amazon Machine Image, source code, and detailed documentation are available at

ADD COMMENTlink modified 8.3 years ago by Istvan Albert ♦♦ 85k • written 8.3 years ago by Malachi Griffith18k
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