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BackgroundImplementation
Software featuresExamplesSummary
Evoker:A visualization tool for genotype intensity data
James A. Morris 1, Joshua C. Randall 2, Julian B. Maller 2 and JeffreyC. Barrett 1
1Statistical and Computational Genetics research group,Wellcome Trust Sanger Institute, Cambridge, UK.
2Wellcome Trust Centre for Human Genetics,University of Oxford, Oxford, UK.
James Morris Evoker
BackgroundImplementation
Software featuresExamplesSummary
What are GWAS?Quality controlEvokerData Challenges
GWAS
James Morris Evoker
BackgroundImplementation
Software featuresExamplesSummary
What are GWAS?Quality controlEvokerData Challenges
Quality control
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ββββββββββββββββββββββββββββββββββ βββββββββββββββββββββββββββββββ βββββββββββββββββββββββ
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Missingness and heterozygosity, by individual
Mean heterozygosity
Fra
ctio
n of
mis
sing
gen
toyp
es
I Rigorous quality control(QC) procedures areessential in GWAS
I Sources of falsepositives include:
I Poor quality DNAI Population structureI Hidden confoundersI Genotyping artifacts
James Morris Evoker
BackgroundImplementation
Software featuresExamplesSummary
What are GWAS?Quality controlEvokerData Challenges
Evoker
I Evoker is an open source program for visualizing genotype intensitycluster plots
I Designed to be integrated into GWAS quality control workflowsI It provides a fast, user-friendly and interactive interfaceI Evoker is a solution to the computational and storage problems
related to working with such large datasetsJames Morris Evoker
BackgroundImplementation
Software featuresExamplesSummary
What are GWAS?Quality controlEvokerData Challenges
Data Challenges
James Morris Evoker
BackgroundImplementation
Software featuresExamplesSummary
Implementation
I Evoker is written in JavaI Utilizes helper scripts written in PerlI Platform specific packages are available for:
I MacI WindowsI Linux
James Morris Evoker
BackgroundImplementation
Software featuresExamplesSummary
Input featuresInteractive features
Input features
James Morris Evoker
BackgroundImplementation
Software featuresExamplesSummary
Input featuresInteractive features
Interactive features
James Morris Evoker
BackgroundImplementation
Software featuresExamplesSummary
Using Evoker to confirm good genotype calls
James Morris Evoker
BackgroundImplementation
Software featuresExamplesSummary
Using Evoker to detect calling errors
James Morris Evoker
BackgroundImplementation
Software featuresExamplesSummary
Using Evoker to detect poor genotyping data
James Morris Evoker
BackgroundImplementation
Software featuresExamplesSummary
Summary
www.sanger.ac.uk/resources/software/evoker/
Open source software under the MIT licenseSource code and files are available here: sourceforge.net/projects/evokerMorris et al. (2010) Evoker: a visualization for genotype intensity data.Bioinformatics 2010 26(14):1786-1787
James Morris Evoker
