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

Dolzhenko, E.; Deshpande, V.; Schlesinger, F.; Krusche, P.; Petrovski, R.; Chen, S.; Emig-Agius, D.; Gross, A.; Narzisi, G.; Bowman, B.; Scheffler, K.; van Vugt, J. J. F. A.; French, C.; Sanchis-Juan, A.; Ibanez, K.; Tucci, A.; Lajoie, B.; Veldink, J. H.; Raymond, L.; Taft, R. J.; Bentley, D. R.; Eberle, M. A.

doi:10.1101/572545

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bioRxiv · 10.1101/572545

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

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Abstract

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.\n\nAvailability and implementationExpansionHunter 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/.\n\nContactmeberle@illumina.com

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Dolzhenko, E., Deshpande, V., Schlesinger, F., Krusche, P., Petrovski, R., Chen, S., Emig-Agius, D., Gross, A., Narzisi, G., Bowman, B., Scheffler, K., van Vugt, J. J. F. A., French, C., Sanchis-Juan, A., Ibanez, K., Tucci, A., Lajoie, B., Veldink, J. H., Raymond, L., Taft, R. J., Bentley, D. R., Eberle, M. A.. 2019-03-09. ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions. https://doi.org/10.1101/572545

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