Skip to content


Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?


Failed to load latest commit information.
Latest commit message
Commit time

Expansion Hunter: a tool for estimating repeat sizes

There are a number of regions in the human genome consisting of repetitions of short unit sequence (commonly a trimer). Such repeat regions can expand to a size much larger than the read length and thereby cause a disease. Fragile X Syndrome, ALS, and Huntington's Disease are well known examples.

Expansion Hunter aims to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat.

Linux and macOS operating systems are currently supported.


Expansion Hunter is provided under the terms and conditions of the PolyForm Strict License 1.0.0. It relies on several third party packages provided under other open source licenses, please see COPYRIGHT.txt for additional details.


Installation instructions, usage guide, and description of file formats are contained in the docs folder.

Companion tools and resources

  • A genome-wide STR catalog containing polymorphic repeats with similar properties to known pathogenic and functional STRs
  • REViewer, a tool for visualizing alignments of reads in regions containing tandem repeats


The method is described in the following papers: