Paper Info
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.
Year
DOI
Venue
2012
10.1093/bioinformatics/bts368
BIOINFORMATICS
Field
DocType
Volume
Data mining,Annotation,Virtual machine,Source code,Computer science,Genomics,Web application,Bioinformatics,Molecular Sequence Annotation,Web service,Cloud computing
Journal
28
Issue
ISSN
Citations 
17
1367-4803
3
PageRank 
References 
Authors
0.40
2
10
Name
Order
Citations
PageRank
Lukas Habegger1171.60
Suganthi Balasubramanian230.40
David Z Chen330.40
Ekta Khurana4202.20
Andrea Sboner59910.28
Arif Ozgun Harmanci6814.30
Joel Rozowsky7766.43
Declan Clarke830.40
Michael Snyder9171.60
Mark Gerstein1020315.32