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Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips

Ritchie, Matthew E.; Liu, Ruijie; Carvalho, Benilton S; Bahlo, Melanie; Foote, Simon; Brown, Matthew A; Cox, Mathew B; McMorran, Brendan; Jensen, Cathy J; Stewart, Graeme; Broadley, Simon; Irizarry, Rafael A.


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...[Show more]

CollectionsANU Research Publications
Date published: 2011
Type: Journal article
Source: BMC Bioinformatics
DOI: 10.1186/1471-2105-12-68
Access Rights: Open Access


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