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Protocols

Evoker specifications

Information


Unique identifier OMICS_22152
Name Evoker
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input format CHIAMO,ILLUMINUS,BIRDSUITE,BEAGLECALL
Output format PNG
Operating system Unix/Linux, Windows
Programming languages Java, Perl
License MIT License
Computer skills Medium
Version 2.4.1
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Jeffrey Barrett
  • person_outline Daniel Rice

Publication for Evoker

Evoker citations

 (15)
library_books

Risk of nontyphoidal Salmonella bacteraemia in African children is modified by STAT4

2018
Nat Commun
PMCID: 5844948
PMID: 29523850
DOI: 10.1038/s41467-017-02398-z

[…] d genotype uncertainty) in SNPTEST2 under additive and genotypic models of association. Following association analysis, genotyped SNPs nominally associated (P < 1 × 10–3) with NTS were inspected with Evoker and SNPs with poor cluster separation excluded from further analysis. Further SNP QC exclusions were applied as follows: model-specific imputation info score <0.8 and Hardy–Weinberg equilibrium […]

library_books

Insights into the genetics of blood pressure in black South African individuals: the Birth to Twenty cohort

2018
BMC Med Genomics
PMCID: 5773038
PMID: 29343252
DOI: 10.1186/s12920-018-0321-6

[…] significantly out of the main cluster in the PCA plots). One SNP (out of all those associated with DBP and SBP) was also disregarded due to poor clustering examined in the cluster plots generated in Evoker []. Checks were also carried out on the phenotype data and corrections were made where inconsistencies were found between the original questionnaires and captured data. […]

library_books

Application of the Physical Disector Principle for Quantification of Dopaminergic Neuronal Loss in a Rat 6 Hydroxydopamine Nigral Lesion Model of Parkinson's Disease

2017
Front Neuroanat
PMCID: 5727600
PMID: 29276478
DOI: 10.3389/fnana.2017.00109

[…] heir attenuated effect on dopamine release on the lesioned side (Ungerstedt and Arbuthnott, ; Hefti et al., ; Carman et al., ; Schwarting and Huston, ). Of the two agents, amphetamine is the stronger evoker of behavioral asymmetry. Thus, rats with more restricted lesions of the SNc do not show rotational asymmetry in response to apomorphine, such that animals with rotation exclusively after amphet […]

library_books

Exome wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling

2017
Hum Mol Genet
PMCID: 5886170
PMID: 28973304
DOI: 10.1093/hmg/ddx328

[…] ity cluster plots were manually inspected for the 5000 SNVs found to have the lowest P-values in a preliminary association test (see below). Where appropriate, genotypes were manually “rescued” using Evoker (version 2.3) (). […]

library_books

Transancestral mapping and genetic load in systemic lupus erythematosus

2017
Nat Commun
PMCID: 5520018
PMID: 28714469
DOI: 10.1038/ncomms16021

[…] efault options were used with one exception: the ‘-nointcutoff’ option was included to allow removal of intensity outliers. Subsequent genotype clusters were viewed against their intensity data using Evoker. Genotype calling was completed in four batches, keeping samples genotyped at the same center in the same batch. Batches were designed to include samples of multiple ancestries when possible to […]

call_split

Association of IFIH1 and pro inflammatory mediators: Potential new clues in SLE associated pathogenesis

2017
PLoS One
PMCID: 5325200
PMID: 28234905
DOI: 10.1371/journal.pone.0171193
call_split See protocol

[…] []. Genotypes were called using Opticall [] using the default options with the addition of -nointcutoff option in order to manually remove intensity outliers. Genotype clusters were determined using Evoker []. Standard quality control procedures were as follows: removal of samples with mean intensity values <0.25 or >3; removal of SNPs and samples with call rates <90%; removal of samples with het […]

Citations

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Evoker institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK

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