Genotype calling for the affymetrix platform

Arne Schillert*, Andreas Ziegler

*Corresponding author for this work
6 Citations (Scopus)


The analysis of high-throughput genotyping data in genome-wide association (GWA) studies has become a standard approach in genetic epidemiology. Data of high quality are crucial for the success of these studies. The first step in the statistical analysis is the generation of genotypes from signal intensities, and several approaches have been proposed for obtaining as accurate genotypes as possible. For the Affymetrix Genome-Wide Human SNP Array 6.0, the genotype calling algorithms Birdseed and CRLMM are commonly used in applications. After a brief description of the statistical methods for both algorithms, their usage is described in detail. Links are provided to the software and to sample code for the installation and execution of the algorithms. Additionally, a suggestion for processing the result files is made.

Original languageEnglish
Title of host publicationStatistical Human Genetics : Methods and Protocols
EditorsRobert Elston, Shuying Sun, Jaya Satagopan
Number of pages11
Publication date2012
ISBN (Print)9781617795541
Publication statusPublished - 2012


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