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Bioinformatics. 2019 May 27. pii: btz431. doi: 10.1093/bioinformatics/btz431. [Epub ahead of print]

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

Author information

1
Illumina Inc., 5200 Illumina Way, San Diego, CA, USA.
2
Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, UK.
3
New York Genome Center, 101 Avenue of the Americas, New York, NY, USA.
4
Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands.
5
Department of Medical Genetics, University of Cambridge, Cambridge, UK.
6
Department of Haematology, University of Cambridge, Cambridge, UK.
7
NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
8
Genomics England, Queen Mary University London, Dawson Hall, London, EC1M 6BQ.

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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