Morris bosc2010 evoker

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  • 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 q q Rigorous quality control 0.6 q qq q q (QC) procedures are Fraction of missing gentoypes 0.5 essential in GWAS Sources of false 0.4 q q q q q positives include: 0.3 q q q Poor quality DNA q Population structure 0.2 q q q q q qq q q qq q q q q qq q q q q q q q q qq q q q qqq q q q q qq qq q q qq q q qq qq q q qq q q q q q q Hidden confounders qq q qq qq q q qqq qq qq q Genotyping artifacts 0.1 q qq q q qqq q qq qq qq qq q qqq q q qqq qqq qqq qq qq qq q q qqq qq q qq qqq q qq q qq qq q qq qq qq q q qq qq q qq q qq q q q q qqq qq qq qqq qqqqq q qq qq q qqq qq qqq qqq q qqqqq qqq qq qqq qqq qqq q qqqqq qqqqqq q qq qqq qqqq qqqq qqqqqq qq qqqqqqq qq qq q qqqqqq q q q qq qq qq qq qqqqqqq q qq q qqqqq q qq qq qqq qqq qq 0.0 qqq qq qqqqq qq qqqqqq qqqqqqqq q q q qq qqq qq qqqqqqqqq qqq qqq q qq qqq qq qq qqq qq qq qq qqqq qqqqqqqq q qqqq qqqq q qq qq qq q qqqqqq qqqqqqqq q q q qq qqq qq qqq q qq qq qqqqq qq qqq qqq q qq qqq qq qq qq qq qq qq q qq qqqq qqqqq q qqq qq qq qq qq qq qqqq qqqq 0.2 0.3 0.4 0.5 0.6 0.7 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