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Protocols

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


github.png

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


download.png

Versioning


No version available

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 citations

 (16)
call_split

Biallelic mutations in mitochondrial tryptophanyl‐tRNA synthetase cause Levodopa‐responsive infantile‐onset Parkinsonism

2018
Clin Genet
PMCID: 5828974
PMID: 29120065
DOI: 10.1111/cge.13172
call_split See protocol

[…] eshift, 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 were validated […]

call_split

A recurrent de novo missense mutation in UBTF causes developmental neuroregression

2018
Hum Mol Genet
PMCID: 5886272
PMID: 29300972
DOI: 10.1093/hmg/ddx435
call_split See protocol

[…] 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 h […]

library_books

Molecular diagnosis of patients with epilepsy and developmental delay using a customized panel of epilepsy genes

2017
PLoS One
PMCID: 5708701
PMID: 29190809
DOI: 10.1371/journal.pone.0188978

[…] ater 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, inherita […]

library_books

Genomic analysis of an infant with intractable diarrhea and dilated cardiomyopathy

2017
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 (). […]

call_split

Evaluating phenotype driven approaches for genetic diagnoses from exomes in a clinical setting

2017
Sci Rep
PMCID: 5647373
PMID: 29044180
DOI: 10.1038/s41598-017-13841-y
call_split See protocol

[…] s effectively reducing to a combined rank across all separate ranks. PhenIX was run utilising the available web server (http://compbio.charite.de/PhenIX/), whilst hiPhive was run using the downloaded Exomiser package. For hiPHIVE and PhenIX, we specified a 0.1% allele frequency cutoff. Exomiser (hiPHIVE) does not include CADD scores as a default but has the option to include them if downloaded loc […]

library_books

Leveraging network analytics to infer patient syndrome and identify causal genes in rare disease cases

2017
BMC Genomics
PMCID: 5558185
PMID: 28812537
DOI: 10.1186/s12864-017-3910-4

[…] leverage integration with other tools to provide this capability (Phevor2 + VAAST [], Phenolyzer + ANNOVAR [], PDR + Ingenuity Variant Analysis), while others offer it as part of the tool (Phen-Gen, Exomiser). Similarly, by partnering or independently, many of these tools (Phevor2 + VAAST, PDR + Ingenuity Variant Analysis, Phen-Gen, Exomiser) can provide family-based analysis involving several sa […]

Citations

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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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