ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions

By E. Dolzhenko, Viraj Deshpande, F. Schlesinger, P. Krusche, Roman Petrovski, Sai Chen, Dorothea Emig-Agius, Andrew M. Gross, G. Narzisi, B. Bowman and 12 more. bioRxiv, 2019

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We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci. Availability and implementation ExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/. Contact meberle@illumina.com

Subfields: Cellular and Molecular Neuroscience, Genetics

View Paper: https://www.semanticscholar.org/paper/a47786d7b1869e918755e32ef559f7db8e042a65