title: VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.
abstract: 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.
  
  
  METHODS
  VAT is implemented in C and PHP. The VAT web service, Amazon Machine Image, source code and detailed documentation are available at vat.gersteinlab.org.
authors: Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA. lukas.habegger@yale.edu
authors: Lukas
authors: L
authors: Habegger
authors: Suganthi
authors: S
authors: Balasubramanian
authors: David Z
authors: DZ
authors: Chen
authors: Ekta
authors: E
authors: Khurana
authors: Andrea
authors: A
authors: Sboner
authors: Arif
authors: A
authors: Harmanci
authors: Joel
authors: J
authors: Rozowsky
authors: Declan
authors: D
authors: Clarke
authors: Michael
authors: M
authors: Snyder
authors: Mark
authors: M
authors: Gerstein
mesh_terms: D014644:Genetic Variation; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D058977:Molecular Sequence Annotation / Q000379:methods*; D012984:Software