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Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

Kim Wong, Thomas M Keane, James Stalker and David J Adams*

Author Affiliations

Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK

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Genome Biology 2010, 11:R128  doi:10.1186/gb-2010-11-12-r128

Published: 31 December 2010

Abstract

We present a pipeline, SVMerge, to detect structural variants by integrating calls from several existing structural variant callers, which are then validated and the breakpoints refined using local de novo assembly. SVMerge is modular and extensible, allowing new callers to be incorporated as they become available. We applied SVMerge to the analysis of a HapMap trio, demonstrating enhanced structural variant detection, breakpoint refinement, and a lower false discovery rate. SVMerge can be downloaded from http://svmerge.sourceforge.net webcite.