SUMMARY: The detection of the structural variants (SVs) using Illumina sequencing of human DNA is not an easy task. Multiple approaches have been proposed; however, all the methods have their limitations. In this article, we present ConsensuSV pipeline that aids the research in complex variant detection. By using consensus meta-approach, eight independent SV callers are being used to identify a uniform set of high-quality SVs. The pipeline works using raw sequencing data and performs all the necessary steps automatically, significantly reducing the researchers' time required for processing the data. The output files contain SVs, single nucleotide polymorphisms and Indels. The pipeline uses luigi framework, allowing the software to be run efficiently and parallelly using the high-performance computing infrastructure. We strongly believe that the software is useful to the scientific community interested in the germline variant detection. AVAILABILITY AND IMPLEMENTATION: https://github.com/SFGLab/ConsensuSV-pipeline. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.