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Bioinformatics Advance Access originally published online on August 6, 2009
Bioinformatics 2009 25(19):2621-2623; doi:10.1093/bioinformatics/btp470
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips

Matthew E. Ritchie 1,*, Benilton S. Carvalho 2, Kurt N. Hetrick 3, Simon Tavaré 4 and Rafael A. Irizarry 2,*

1Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville Victoria 3052, Australia, 2Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, North Wolfe Street, Baltimore, MD 21205, 3Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA and 4Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK

*To whom correspondence should be addressed.


  Abstract

Summary: Illumina produces a number of microarray-based technologies for human genotyping. An Infinium BeadChip is a two-color platform that types between 105 and 106 single nucleotide polymorphisms (SNPs) per sample. Despite being widely used, there is a shortage of open source software to process the raw intensities from this platform into genotype calls. To this end, we have developed the R/Bioconductor package crlmm for analyzing BeadChip data. After careful preprocessing, our software applies the CRLMM algorithm to produce genotype calls, confidence scores and other quality metrics at both the SNP and sample levels. We provide access to the raw summary-level intensity data, allowing users to develop their own methods for genotype calling or copy number analysis if they wish.

Availability and Implementation: The crlmm Bioconductor package is available from http://www.bioconductor.org. Data packages and documentation are available from http://rafalab.jhsph.edu/software.html.

Contact: mritchie{at}wehi.edu.au; rafa{at}jhu.edu

Associate Editor: Jeffrey Barrett

Received on May 18, 2009; revised on July 8, 2009; accepted on July 28, 2009

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B. S. Carvalho, T. A. Louis, and R. A. Irizarry
Quantifying uncertainty in genotype calls
Bioinformatics, January 15, 2010; 26(2): 242 - 249.
[Abstract] [Full Text] [PDF]


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