Exomiser statistics

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Exomiser specifications

Information


Unique identifier OMICS_05448
Name Exomiser
Interface Web user interface
Restrictions to use None
Input data The called variants resulting from exome sequencing of a rare disease patient and, optionally, other affected and unaffected family members.
Input format VCF
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Download


Documentation


Maintainer


  • person_outline Peter Robinson <>

Additional information


Previous version: https://www.sanger.ac.uk/science/tools/exomiser http://exomiser.github.io/Exomiser/

Information


Unique identifier OMICS_05448
Name Exomiser
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data The called variants resulting from exome sequencing of a rare disease patient and, optionally, other affected and unaffected family members.
Input format VCF
Output data An HTML page that summarizes the results of the analysis.
Operating system Unix/Linux
Programming languages Java
License GNU Affero General Public License version 3
Computer skills Advanced
Version 10.1.0
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Peter Robinson <>

Additional information


Previous version: https://www.sanger.ac.uk/science/tools/exomiser http://exomiser.github.io/Exomiser/

Publications for Exomiser

Exomiser in pipelines

 (4)
2017
PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] the sequence of the protein, they were considered directly as the maximum pavar score = 7. all the variants with a score ≥5 were not filtered, and they were considered as candidate variants.exomiser v2 softwareexomiser v2 prioritizes snvs by comparing the phenotype across species, according to the inheritance pattern, using the mouse and fish as a model organism phenotype []. variant […]

2017
PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] the sequence of the protein, they were considered directly as the maximum pavar score = 7. all the variants with a score ≥5 were not filtered, and they were considered as candidate variants., exomiser v2 software, exomiser v2 prioritizes snvs by comparing the phenotype across species, according to the inheritance pattern, using the mouse and fish as a model organism phenotype []. variant […]

2017
PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] [0, 1], according to top 10, 20, or 50. roc curves were generated to determine the ability to predict real causal variants based on models consisting of the combination of the five systems (pavar, exomiser v2, vaast-phevor, cadd, and fathmm) and each individual system. in all the cases, the analyses were performed for the top 10, 20, and 50 ranked variants and using different control datasets […]

2015
PMCID: 4916229
PMID: 26562225
DOI: 10.1038/gim.2015.137

[…] previously shown that phenotypic semantic similarity analyses on copy-number variations help explain the genetic contribution to patient phenotypes. finally, we will need to adapt future versions of exomiser to assess the significantly greater number of variations identified by whole-genome sequencing data and develop effective methods of prioritizing the mainly intronic and intergenic […]


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Exomiser in publications

 (20)
PMCID: 5828974
PMID: 29120065
DOI: 10.1111/cge.13172

[…] stopgain, stoploss, startloss, inframe), proximity to splice sites (within 20 base pairs of a canonical splice site into the intron, or 5 base pairs into the exon), cadd v1.3 phred scores and exomiser. the quality of alignment and genotype call of variants were checked using the integrative genome viewer (https://www.broadinstitute.org/igv/home). the final candidate variants […]

PMCID: 5886272
PMID: 29300972
DOI: 10.1093/hmg/ddx435

[…] stop gain, stop loss, start loss, in frame), proximity to splice sites (within 20 base pairs of a canonical splice site into the intron, or 5 base pairs into the exon), cadd v1.3 phred scores () and exomiser (). prioritized variants with potential coding effects had cadd phred scores ≥ 5. splice site variants did not undergo the cadd phred score filter of ≥ 5 because non-coding variants usually […]

PMCID: 5708701
PMID: 29190809
DOI: 10.1371/journal.pone.0188978

[…] than 0.85 are interpreted as probably damaging. sift scores of less than 0.05 are predicted to be deleterious and those greater than or equal to 0.05 are predicted to be tolerated. also, we used exomiser (http://www.sanger.ac.uk/resources/databases/exomiser/) [], an online tool that functionally annotates and prioritises mutated genes using variant frequency, predicted pathogenicity, […]

PMCID: 5701300
PMID: 28701297
DOI: 10.1101/mcs.a002055

[…] from the hpo database version 01 2016 () for the classes directly associated with the input hpo identifiers and their subclasses and supplemented with gene lists from the literature (). in addition, exomiser v6.0.0 phenotype scores were calculated for each gene based on cross-species phenotype comparisons with mouse and zebrafish mutants and protein–protein interactomes ()., for clinvar […]

PMCID: 5647373
PMID: 29044180
DOI: 10.1038/s41598-017-13841-y

[…] variant at between 1 and 10 in 85% of these cases. this is a significantly higher proportion than the combined results from five alternative methods tested (p = 0.003). the next best method is exomiser (hiphive), in which the causal variant is ranked 1–10 in 25% of cases. the widely different targets of these methods (more clinical focus, considering known mendelian genes, in phenix, […]


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Exomiser institution(s)
Skarnes Faculty Group, Wellcome Trust Sanger Institute, Hinxton, UK; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany; Berlin Institute for Health, Berlin, Germany; Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Labor Berlin - Charité Vivantes, Humangenetik, Berlin, Germany; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; The National Institutes of Health (NIH) Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA; Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Berlin, Germany
Exomiser funding source(s)
Supported by the Bundesministerium für Bildung und Forschung (BMBF; project no. 0313911), the European Community’s Seventh Framework Programme (grant agreement no. 602300; SYBIL) and NIH grant no. 5R24OD011883 (Monarch Initiative).

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