Wellcome Trust Case Control Consortium

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Available software

Software developed in the course of WTCCC is available for download. Technical queries and feedback should be sent directly to the authors.

Cel Quantile Normalisation

(Hin-Tak Leung, work undertaken whilst at Cambridge Institute for Medical Research)

Various normalisation-related programs for pre-processing Affymetrix 500K chip data prior to calling by Chiamo++. Version 2007-01-09. Users will also need to download the 500K Chip Definition (CDF) files from Affymetrix.

This, along with snpMatrix (see below), the Bonsai plug-in for Illumina BeadStudio and the R package RFlowJo are all available from SourceForge: http://outmodedbonsai.sourceforge.net.


(Jonathan Marchini et al, Department of Statistics, University of Oxford)

Chiamo, along with other software developed for Genome-wide Association Study, is available direct from Jonathan.


(David Clayton, DRF/WT Diabetes and Inflammation Laboratory and Hin-Tak Leung)

An R package for analysis of genome-wide association studies. This is now distributed as part of the BioConductor project: http://www.bioconductor.org. A preliminary description of the package is given by: Clayton, D.G. and Leung, Hin-Tak (2007) An R package for analysis of whole-genome association studies. Human Heredity 64:45-51.