Journal article
Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips
ME Ritchie, R Liu, BS Carvalho, RA Irizarry, M Bahlo, DR Booth, SA Broadley, MA Brown, SJ Foote, LR Griffiths, TJ Kilpatrick, J Lechner-Scott, P Moscato, VM Perreau, JP Rubio, RJ Scott, J Stankovich, GJ Stewart, BV Taylor, J Wiley Show all
BMC Bioinformatics | BMC | Published : 2011
Open access
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.Results: In general, differences in accuracy are relatively small between the methods evaluated, although CRLMM and GenoSNP were found to consistently outperform GenC..
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Awarded by National Institutes of Health
Funding Acknowledgements
This work was supported by NHMRC Program grant 406657, NHMRC IRIISS grant 361646 and a Victorian State Government OIS grant (MER, RL), and NIH grants R01GM083084, R01RR021967 and P41HG004059 (BSC, RAI).