SV-AUTOPILOT pipeline. Illumina pair-end NGS data in the form of a fastq file is submitted to the pipeline for SV analysis along with a genomic reference sequence. A quality report is provided by Fastqc, and Sickle is used for trimming low quality reads. Modularity allows for a choice of read aligner and SV tools. Samtools flagstat is run to evaluate the quality of the mapping. Each tool’s output is converted to a VCF format, unless already provided by the program, for downstream use by the researcher. For those wanting to benchmark tool performance, the performance metrics for the tools can be compared in the PDF report provided. Finally, when using multiple tools as part of a pipeline leading to SV validation, the option to merge SV calls according to the statistical method provided here is available to enrich the call set with true calls by merging results and reducing false-positive calls.