@inbook{579ff5ab5a04451d81f3a0e6bb88eb0f,
title = "Quality control for genome-wide association studies",
abstract = "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.",
keywords = "Genome-wide association studies, Illumina, Quality control, R statistics",
author = "Cedric Gondro and Lee, \{Seung Hwan\} and Lee, \{Hak Kyo\} and Porto-Neto, \{Laercio R.\}",
year = "2013",
doi = "10.1007/978-1-62703-447-0\_5",
language = "English",
isbn = "9781627034463",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "129--147",
booktitle = "Genome-Wide Association Studies and Genomic Prediction",
}