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.