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. 2019 Nov 1;35(22):4754-4756.
doi: 10.1093/bioinformatics/btz431.

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

Egor Dolzhenko  1 , Viraj Deshpande  1 , Felix Schlesinger  1 , Peter Krusche  2 , Roman Petrovski  2 , Sai Chen  1 , Dorothea Emig-Agius  1 , Andrew Gross  1 , Giuseppe Narzisi  3 , Brett Bowman  1 , Konrad Scheffler  1 , Joke J F A van Vugt  4 , Courtney French  5 , Alba Sanchis-Juan  6   7 , Kristina Ibáñez  8 , Arianna Tucci  8 , Bryan R Lajoie  1 , Jan H Veldink  4 , F Lucy Raymond  5 , Ryan J Taft  1 , David R Bentley  2 , Michael A Eberle  1
Affiliations

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

Egor Dolzhenko et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
Overview of ExpansionHunter. (a) A locus definition is read from the variant catalog file. (b) Sequence graph is constructed according to its specification in the variant catalog. (c) Relevant reads are extracted from the input binary alignment/map file. (d) Reads are aligned to the graph. (e) Alignments are pieced together to genotype each variant
See this image and copyright information in PMC

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