BioinformaticsBioinformaticsPeer-reviewed journal article
ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions
Egor DolzhenkoiD, Viraj Deshpande, Felix J. Schlesinger, Peter KruscheiD, Roman Petrovski, Sai CheniD, Dorothea Emig-Agius, Andrew M. GrossiD, Giuseppe NarzisiiD, Brett N. BowmaniD, Konrad ScheffleriD, Joke J.F.A. van VugtiD, Courtney E. FrenchiD, Alba Sanchis‐JuaniD, Kristina IbáñeziD, Arianna TucciiD, Bryan R. LajoieiD, Jan Herman VeldinkiD, Frances Lucy RaymondiD, Ryan J. TaftiD, David Bentley, Michael A. EberleiD
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Abstract
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.\n\nAvailability and implementationExpansionHunter 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/.\n\nContactmeberle@illumina.com
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