An overview of the SVMerge pipeline. SVMerge uses a suite of software tools to detect structural variants (SVs) from mapped reads. The calls are filtered, merged and then validated computationally by local de novo assembly. The output is in BED format, allowing for easy downstream analysis or viewing in a genome browser. The SVMerge pipeline is extendable so that calls made by other software can be included in the downstream analysis. BAM, Binary Alignment/Map format.