R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.

Abstract

Illumina produces a number of microarray-based technologies for human genotyping. An Infinium BeadChip is a two-color platform that types between 10(5) and 10(6) single nucleotide polymorphisms (SNPs) per sample. Despite being widely used, there is a shortage of open source software to process the raw intensities from this platform into genotype calls. To this end, we have developed the R/Bioconductor package crlmm for analyzing BeadChip data. After careful preprocessing, our software applies the CRLMM algorithm to produce genotype calls, confidence scores and other quality metrics at both the SNP and sample levels. We provide access to the raw summary-level intensity data, allowing users to develop their own methods for genotype calling or copy number analysis if they wish. The crlmm Bioconductor package is available from http://www.bioconductor.org. Data packages and documentation are available from http://rafalab.jhsph.edu/software.html.