The document discusses Evoker, a visualization tool for genotype intensity data from genome-wide association studies (GWAS). It provides background on GWAS and highlights the importance of rigorous quality control procedures for GWAS to eliminate sources of false positives like poor quality DNA, population structure, and genotyping artifacts. The document then discusses Evoker's implementation and software features for visualizing quality control metrics and genotype intensity data to assist with quality control checks.

1. Background
Implementation
Software features
Examples
Summary
Evoker:
A visualization tool for genotype intensity data
James A. Morris 1 , Joshua C. Randall 2 , Julian B. Maller 2 and Jeffrey
C. Barrett 1
1
Statistical and Computational Genetics research group,
Wellcome Trust Sanger Institute, Cambridge, UK.
2
Wellcome Trust Centre for Human Genetics,
University of Oxford, Oxford, UK.
James Morris Evoker

2. Background
What are GWAS?
Implementation
Quality control
Software features
Evoker
Examples
Data Challenges
Summary
GWAS
James Morris Evoker

3. Background
What are GWAS?
Implementation
Quality control
Software features
Evoker
Examples
Data Challenges
Summary
Quality control
Missingness and heterozygosity, by individual
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Fraction of missing gentoypes
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Sources of false
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Mean heterozygosity
James Morris Evoker

4. Background
What are GWAS?
Implementation
Quality control
Software features
Evoker
Examples
Data Challenges
Summary
Evoker
Evoker is an open source program for visualizing genotype intensity
cluster plots
Designed to be integrated into GWAS quality control workflows
It provides a fast, user-friendly and interactive interface
Evoker is a solution to the computational and storage problems
related to working with such large datasets
James Morris Evoker

5. Background
What are GWAS?
Implementation
Quality control
Software features
Evoker
Examples
Data Challenges
Summary
Data Challenges
James Morris Evoker

6. Background
Implementation
Software features
Examples
Summary
Implementation
Evoker is written in Java
Utilizes helper scripts written in Perl
Platform specific packages are available for:
Mac
Windows
Linux
James Morris Evoker

7. Background
Implementation
Input features
Software features
Interactive features
Examples
Summary
Input features
James Morris Evoker

8. Background
Implementation
Input features
Software features
Interactive features
Examples
Summary
Interactive features
James Morris Evoker

9. Background
Implementation
Software features
Examples
Summary
Using Evoker to confirm good genotype calls
James Morris Evoker

10. Background
Implementation
Software features
Examples
Summary
Using Evoker to detect calling errors
James Morris Evoker

11. Background
Implementation
Software features
Examples
Summary
Using Evoker to detect poor genotyping data
James Morris Evoker

12. Background
Implementation
Software features
Examples
Summary
Summary
www.sanger.ac.uk/resources/software/evoker/
Open source software under the MIT license
Source code and files are available here: sourceforge.net/projects/evoker
Morris et al. (2010) Evoker: a visualization for genotype intensity data.
Bioinformatics 2010 26(14):1786-1787
James Morris Evoker