ExomeDepth pipeline

ExomeDepth specifications


Unique identifier OMICS_05443
Name ExomeDepth
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1.10
Stability Stable
Source code URL https://cran.r-project.org/src/contrib/ExomeDepth_1.1.10.tar.gz
Maintained Yes



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  • person_outline Vincent Plagnol <>

Publication for ExomeDepth

ExomeDepth citation

PMCID: 4422538

[…] human genome assembly hg19 (ucsc genome browser) was done with burrows-wheeler aligner (bwa, v.0.7.5). detection of genetic variation was performed using samtools (v 0.1.18), pindel (v 0.2.4┬át), and exomedepth (v1.0.0). variant filtering was based on a presumed autosomal-recessive mode of inheritance and focused on homozygous and predictively compound heterozygous rare nonsynonymous variants […]

ExomeDepth institution(s)
UCL Genetics Institute, UCL, London, UK; Department of Medicine, University of Cambridge, Cambridge, UK; UCL CoMPLEX program, London, UK; UCL Institute of Neurology, UCL, London, UK; Royal London Hospital, London, UK; Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK; Molecular Immunology Unit, Wolfson Centre for Gene Therapy of Childhood Disease, UCL Institute of Child Health, Great Ormond Street Hospital for Children, London, UK; Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital, Cambridge, UK
ExomeDepth funding source(s)
Supported by a Wellcome Trust Senior Research Fellow in Basic Biomedical Science (095198/Z/10/Z); the Wellcome Trust grant (088838/Z/09/Z), the Royal Society Research grant RG090638, the EU FP7 grant (261441) (PEVNET project) and the ERC Starting grant (260477); the NIHR Cambridge Biomedical Research Centre; MRC research grant (G1001158) and the NIHR Moorfields Biomedical Research Council grant.

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