ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions
bioRxiv (Cold Spring Harbor Laboratory)2019
Citations Over Time
Egor Dolzhenko, Viraj Deshpande, Felix Schlesinger, Peter Krusche, Roman Petrovski, Sai Chen, Dorothea Emig-Agius, Andrew M. Gross, Giuseppe Narzisi, Brett Bowman, Konrad Scheffler, Joke J.F.A. van Vugt, Courtney E. French, Alba Sanchis‐Juan, Kristina Ibáñez, Arianna Tucci, Bryan R. Lajoie, Jan H. Veldink, Lucy Raymond, Ryan J. Taft, David Bentley, Michael A. Eberle
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/ . Contact meberle@illumina.com
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