Expansion Hunter is a tool for targeted genotyping of short tandem repeats and flanking variants. It operates by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat. Newer versions of the program provide limited support for insertions, deletions, and substitutions.
In order to use Expansion Hunter you need to (1) download the latest release or build the program from source, (2) obtain a set of files specifying repeat regions of interest, and (3) have a BAM or a CRAM file with alignments of reads from a PCR-free WGS sample.
The following sections will help you to get started.