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

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

SUBMITTER: Dolzhenko E 

PROVIDER: S-EPMC6853681 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature