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

Kim Wong, Thomas M Keane, James Stalker, David J Adams
2010 Genome Biology  
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.
doi:10.1186/gb-2010-11-12-r128 pmid:21194472 pmcid:PMC3046488 fatcat:yyexy5ow7nd2ngij5lzd23tyea