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BMCBI
2011

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

10 years 6 months ago
Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips
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 GenCall. The performance of Illuminus is heavily dependent on sample size, with lower no call rates and improved accuracy as the number of samples available increases. For X chromosome SNPs, methods with sex-dependent models (Illuminus, CRLMM) perform better than methods which ignore gender informat...
Matthew E. Ritchie, Ruijie Liu, Benilton Carvalho,
Added 12 May 2011
Updated 12 May 2011
Type Journal
Year 2011
Where BMCBI
Authors Matthew E. Ritchie, Ruijie Liu, Benilton Carvalho, Rafael A. Irizarry
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