Others have discussed quality control procedures for genotypic data [13-16]. The goal of this manuscript is a tutorial to instruct investigators on QC procedures that should be performed prior to GWAS data analysis. The procedures discussed here were developed by the genomics group of the eMERGE network, where phenotyping and other sample information is obtained through sophisticated mining of the EMR. This protocol can be applied to many GWAS studies, regardless of phenotyping strategy. Given that most of the genotyping data available for GWAS is currently SNP-based, we will limit our discussion to these biallelic markers, and QC procedures for CNV analysis will not be discussed here. Figure 1 shows a flowchart overview of the entire QC process, where each step is discussed in detail in the following sections.
