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Updated: Sep 10, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read
Shunichi Kosugi1,2,3,4, Chikashi Terao5,6,7
1Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems Center for Genome Informatics, 1111, Yata, Mishima, Shizuoka, 411-8540, Japan. shunichi.kosugi@nig.ac.jp.
Abstract:
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.
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