This chapter overviews the quality control (QC) issues for SNP-based genotyping methods used in genome-wide association studies. The main metrics for evaluating the quality of the genotypes are discussed followed by a worked out example of QC pipeline starting with raw data and finishing with a fully filtered dataset ready for downstream analysis. The emphasis is on automation of data storage, filtering, and manipulation to ensure data integrity throughput the process and on how to extract a global summary from these high dimensional datasets to allow better-informed downstream analytical decisions. All examples will be run using the R statistical programming language followed by a practical example using a fully automated QC pipeline for the Illumina platform. © Springer Science+Business Media, LLC 2013.
CITATION STYLE
Gondro, C., Lee, S. H., Lee, H. K., & Porto-Neto, L. R. (2013). Quality control for genome-wide association studies. Methods in Molecular Biology, 1019, 129–147. https://doi.org/10.1007/978-1-62703-447-0_5
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