XHMM pipeline

XHMM specifications


Unique identifier OMICS_03956
Alternative name eXome-Hidden Markov Model
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements gcc, pthread, lapack, Gengetopt
Maintained Yes



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  • person_outline Shaun Purcell <>
  • person_outline Menachem Fromer <>

Publication for eXome-Hidden Markov Model

XHMM citation

PMCID: 4989049

[…] (illumina). candidate snvs that could be related to the clinical features of patients with developmental delays were further analyzed through a family-based approach using parental samples., the xhmm was used to quantify copy numbers throughout the genome.4,7,9 briefly, bam files generated from the gatk data-processing pipeline were accumulated and the depth of coverage was calculated. […]

XHMM institution(s)
Division of Psychiatric Genomics, Mount Sinai School of Medicine, New York, NY, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA; Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Department of Psychological Medicine and Neurology, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
XHMM funding source(s)
Supported by National Institute of Health grants RC2MH089905 and R01HG005827 and by the Sylvan Herman Foundation.

XHMM review

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Tristan Dubos

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If you are looking for CNV in panel and got more than 50 samples it work great and fast !