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

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 GenCall. The performance of Illuminus is heavily dependent on sample size, with lower no c

SUBMITTER: Ritchie ME 

PROVIDER: S-EPMC3063825 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature