Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips |
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| Authors: | Matthew?E?Ritchie Ruijie?Liu Benilton?S?Carvalho The Australia New Zealand Multiple Sclerosis Genetics Consortium Rafael?A?Irizarry |
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| Affiliation: | (1) Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, 3052 Parkville, Victoria, Australia;(2) Department of Medical Biology, The University of Melbourne, 3010 Parkville, Victoria, Australia;(3) Department of Oncology, CRUK Cambridge Research Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, CB2 0RE Cambridge, UK;(4) Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, North Wolfe Street E3035, 21205 Baltimore, MD, USA |
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| Abstract: | Background Illumina's Infinium SNP BeadChips are extensively used in both small and large-scale genetic studies. A fundamental step in any analysis is the processing of raw allele A and allele B intensities from each SNP into genotype calls (AA, AB, BB). Various algorithms which make use of different statistical models are available for this task. We compare four methods (GenCall, Illuminus, GenoSNP and CRLMM) on data where the true genotypes are known in advance and data from a recently published genome-wide association study. |
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