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ExpansionHunter specifications


Unique identifier OMICS_21520
Name ExpansionHunter
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Indexed file containing aligned reads from a PCR-free WGS sample, A file with a reference genome assembly (which must be identical to the one used for aligning the reads), Repeat specification files.
Input format (BAM,CRAM)+(FASTA,JSON)
Output data A file containing repeat genotypes along with information and a log file with alignments of spanning and flanking reads and sequences of in-repeat reads.
Output format VCF,JSON
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.3.5
Stability Stable
GCC, clang, CMake, Boost C++ Libraries
Source code URL https://codeload.github.com/Illumina/ExpansionHunter/zip/v2.5.3
Maintained Yes




No version available


  • person_outline Michael A. Eberle

Additional information


Publication for ExpansionHunter

ExpansionHunter citations


A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies

Front Genet
PMCID: 5941971
PMID: 29770143
DOI: 10.3389/fgene.2018.00155

[…] repeatseq (highnam et al., ) lobstr (gymrek et al., ), revister (tae et al., ), vntrseek (gelfand et al., ), myflq (van neste et al., ). pstr finder (lee et al., ), str-fm (fungtammasan et al., ), expansionhunter (dolzhenko et al., ), hipstr (willems et al., ), and tredparse (tang et al., ). recent surveys in cao et al. () and gymrek () compare the performance of many of these tools., catalogs […]


Profiling of Short Tandem Repeat Disease Alleles in 12,632 Human Whole Genomes

Am J Hum Genet
PMCID: 5673627
PMID: 29100084
DOI: 10.1016/j.ajhg.2017.09.013

[…] an str locus. owing to the short length of illumina reads (100–150 bases), this imposes a major limitation on the length of str alleles that can be identified. a more recently developed str caller, expansionhunter, incorporates additional evidence beyond spanning reads., it is also possible to estimate length variation at an str by combining information from a prior estimate and the observed […]

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ExpansionHunter institution(s)
Illumina Inc., San Diego, CA, USA; Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands; Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, UK; Repositive Ltd., Future Business Centre, Cambridge, UK; Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; New York Genome Center, New York, NY, USA; SURFsara, Amsterdam, Netherlands; Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Republic of Ireland; Department of Neurology, Beaumont Hospital, Dublin, Republic of Ireland; Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK; University of Southampton, Southampton, UK; Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK; Columbia University, New York, NY, USA; Hereditary Disease Foundation, New York, NY, USA; The US-Venezuela Collaborative Research Group; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
ExpansionHunter funding source(s)
Supported in part by the Dutch national e-infrastructure with the support of SURF Cooperative; NIH/NINDS P01 NS084974 (MvB, RR), R01 NS080882 (MvB, RR); the Thierry Latran Foundation (MAvE, JHV, GPT); the Netherlands Organization for Health Research and Development (Veni scheme, MAvE); the ALS Foundation Netherlands; the MND Association (UK) (Project MinE); and the W. M. Keck Foundation through the grant “Finding Genetic Modifiers As Avenues to Developing New Therapeutics”; the European Community's Health Seventh Framework Programme (FP7/2007-2013) and Horizon 2020 Programme (H2020-PHC-2014-two-stage; grant agreement number 633413); ZonMW under the framework of E-Rare-2; the ERA Net for Research on Rare Diseases (PYRAMID); The EU Joint Programme–Neurodegenerative Disease Research (JPND) project (STRENGTH, SOPHIA, ALS-CarE); JPND: UK, Medical Research Council (MR/L501529/1) and (ES/L008238/1); Ireland, Health Research Board; Netherlands, ZonMw.

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