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ExomeDepth specifications

Information


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
Requirements
methods, IRanges, Rsamtools, Biostrings, GenomicAlignments, knitr, R(≥3.3.0), GenomicRanges(≥1.23.0), aod, VGAM(≥0.8.4)
Source code URL https://cran.r-project.org/src/contrib/ExomeDepth_1.1.10.tar.gz
Maintained Yes

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Maintainer


  • person_outline Vincent Plagnol <>

Publication for ExomeDepth

ExomeDepth in pipelines

 (4)
2017
PMCID: 5800348
PMID: 29074561
DOI: 10.1136/jmedgenet-2017-104791

[…] calling was performed. we have described the methodology employed for the detection and clinical analysis of snvs and indels previously. cnv detection was performed using standard parameters for exomedepth v.1.1.6. exomedepth was presented with sets of aligned and non-duplicate sequencing reads in a binary sequence alignment/map (bam) file format that were matched by gender […]

2017
PMCID: 5886296
PMID: 29228333
DOI: 10.1093/hmg/ddx422

[…] the charity open access fund (coaf) to the university of leeds., babraham bioinformatics: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, cut adapt: https://github.com/marcelm/cutadapt, exomedepth: https://cran.r-project.org/web/packages/exomedepth/, picard: http://broadinstitute.github.io/picard/, vcfhacks: https://github.com/gantzgraf/vcfhacks; all web-sites date last accessed […]

2016
PMCID: 5409526
PMID: 28459104
DOI: 10.21956/wellcomeopenres.10849.r20638

[…] appropriate probe kits and protocols from mrc holland, as previously described ., we performed a review of the available methods and elected to build a tool through modification and optimisation of exomedepth v.1.0.0 . this tool was chosen because of its performance and because it was open source and easy to modify. we have called the tool decon for detection of exon copy number., to create […]

2015
PMCID: 4504554
PMID: 26166082
DOI: 10.1097/MD.0000000000001073

[…] genomics viewer was used to view the mapping and annotation of sequences. pindel was used for detecting structural variants such as large deletions/insertions, inversions, and duplications, and exomedepth for detecting copy number variants., variants with allele frequencies above 5% in both the 1000 genomes project and the nhlbi-esp 6500 exome project (http://evs.gs.washington.edu/evs/) […]


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ExomeDepth in publications

 (37)
PMCID: 5876250
PMID: 29628935
DOI: 10.3389/fgene.2018.00080

[…] through use of read depth information and maximum penalized likelihood estimation (mple) (chen et al., ). cnvs can also be identified from targeted ngs data using a popular software package called exomedepth. the sensitivity and specificity of exomedepth v1.1.16 were determined to be 100% and 99.8%, respectively, validating this technique as an appropriate method for detection of cnvs […]

PMCID: 5931241
PMID: 29453195
DOI: 10.1136/jmedgenet-2017-104954

[…] files and annotated using a variant effect predictor, including those with minor allele frequencies (maf), in public databases and the beijing genomics institute (bgi) in-house databases. we used exomedepth software to detect the cnvs of this pedigree. by setting the parameters and following the instructions, we obtained rare cnvs from exome sequencing data. under the assumption […]

PMCID: 5796507
PMID: 29390993
DOI: 10.1186/s12920-018-0320-7

[…] and deletions was conducted using the pindel and manta algorithms, and both results were finally crosschecked. read-depth-based detection of structural rearrangements was conducted using the exomedepth software. chromosomal copy number variations (cnvs) detected by exomedepth were further crosschecked using our custom pipeline; this retrieved base-level depth-of-coverage for each bam […]

PMCID: 5793772
PMID: 29258992
DOI: 10.1101/mcs.a002139

[…] exome variant server (evs) (http://evs.gs.washington.edu/evs/), and exome aggregation consortium (exac) (http://exac.broadinstitute.org/)., additionally, three widely used cnv callers, exomedepth (), xhmm (), and conifer (), were used to obtain highly confident calls based on the consensus between the callers (see supplemental material; supplemental file 1 for called cnvs […]

PMCID: 5769462
PMID: 29338689
DOI: 10.1186/s12885-017-3940-y

[…] insertion-deletions, and copy number variants (cnvs) in each gene. split-read-based detection of large insertions and deletions was conducted using the pindel and manta algorithms. cnvs detected by exomedepth software [] were further crosschecked with our custom pipelines, which retrieved base-level depth of coverage for each binary alignment map (bam) file using samtools software […]


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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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