Genotype Calling for the Illumina Platform

Genome-wide association studies have been made possible because of advancements in the design of genotyping technologies to assay a million or more single nucleotide polymorphisms (SNPs) simultaneously. This has resulted in the introduction of automated and unsupervised statistical approaches for translating the probe hybridization intensities into the actual genotype calls. This chapter aims to provide an introduction to this process of genotype calling, highlighting in particular the design and approach used for the Illumina BeadArray platforms that are commonly used in large-scale genetic studies. The chapter also provides detailed instructions for preparing the input files required as well as the actual Linux commands and options to execute the ILLUMINUS software. Finally, it concludes with a brief exposition on the different outcomes from genotype calling and the use of perturbation analysis for identifying SNPs with erroneous genotype calls.