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 …