Egor Dolzhenko, Viraj Deshpande, Felix Schlesinger, Peter Krusche, Roman Petrovski, Sai Chen, Dorothea Emig-Agius, Andrew Gross, Giuseppe Narzisi, Brett Bowman, Konrad Scheffler, Joke J. F. A. {van Vugt}, Courtney French, Alba Sanchis-Juan, Kristina Ibanez, Arianna Tucci, Bryan Lajoie, Jan H. Veldink, F. Lucy Raymond, Ryan J. Taft, David R. Bentley, Michael A. Eberle. ExpansionHunter: A sequence-graph based tool to analyze variation in short tandemrepeat regions. Bioinformatics, 2019.
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Abstract:
SUMMARY: 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/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.