TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data

Tandem repeat copy number variations (TR-CNVs), structural variations (SVs), and short indels have been responsible for many diseases and traits, but no tools exist to distinguish and detect these variants. In this study, we developed a computational tool, TRsv, to distinguish and detect TR-CNVs, SVs, and short indels using long reads. In evaluation with simulated and real datasets, TRsv outperformed existing tools for detection of TR-CNVs and indels and performed equally well for detection of SVs. We demonstrated genome-wide detection of TR-CNVs, including variants associated with gene expression, disease, and quantitative traits, using 160 long-read whole genome sequencing data and TRsv.