ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions.
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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.
SUBMITTER: Dolzhenko E
PROVIDER: S-EPMC6853681 | biostudies-literature | 2019 Nov
REPOSITORIES: biostudies-literature
Publications
ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions.
Dolzhenko Egor E Deshpande Viraj V Schlesinger Felix F Krusche Peter P Petrovski Roman R Chen Sai S Emig-Agius Dorothea D Gross Andrew A Narzisi Giuseppe G Bowman Brett B Scheffler Konrad K van Vugt Joke J F A JJFA French Courtney C Sanchis-Juan Alba A Ibáñez Kristina K Tucci Arianna A Lajoie Bryan R BR Veldink Jan H JH Raymond F Lucy FL Taft Ryan J RJ Bentley David R DR Eberle Michael A MA
Bioinformatics (Oxford, England) 20191101 22
<h4>Summary</h4>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.<h4>Availability and implementation</ ...[more]
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