{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:21:19Z","timestamp":1764688879095},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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.<\/jats:p>\n               <jats:p>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 vat.gersteinlab.org.<\/jats:p>\n               <jats:p>Contact: lukas.habegger@yale.edu or mark.gerstein@yale.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts368","type":"journal-article","created":{"date-parts":[[2012,6,29]],"date-time":"2012-06-29T00:52:19Z","timestamp":1340931139000},"page":"2267-2269","source":"Crossref","is-referenced-by-count":62,"title":["VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment"],"prefix":"10.1093","volume":"28","author":[{"given":"Lukas","family":"Habegger","sequence":"first","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, 3Department of Computer Science, Yale University, New Haven, CT 06520, USA, 4Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, 5Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, 6Department of Chemistry, Yale University, New Haven, CT 06520 and 7Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suganthi","family":"Balasubramanian","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, 3Department of Computer Science, Yale University, New Haven, CT 06520, USA, 4Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, 5Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, 6Department of Chemistry, Yale University, New Haven, CT 06520 and 7Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, 3Department of Computer Science, Yale University, New Haven, CT 06520, USA, 4Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, 5Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, 6Department of Chemistry, Yale University, New Haven, CT 06520 and 7Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David Z.","family":"Chen","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, 3Department of Computer Science, Yale University, New Haven, CT 06520, USA, 4Department of Pathology and Laboratory Medicine, Weill Cornell 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