The eMERGE (electronic MEdical Records and GEnomics) Network is an NHGRI-supported consortium of five institutions charged with exploring the utility of DNA repositories coupled to Electronic Medical Record (EMR) systems for advancing discovery in genome science [12]. Genome-wide genotyping has been performed on ~17,000 samples across the eMERGE network at the Broad Institute and at the Center for Inherited Disease Research (CIDR) using the Illumina 660W-Quad or 1M-Duo Beadchips. Each study site is conducting a GWAS, in addition to a number of cross-network analyses. These studies adhere to NIH’s data sharing policies, and all data generated in this study will be available on dbGaP [11]. Due to the complexity involved in a single site GWAS, in addition to the combining of data and results across study sites, it became clear that a unified QC pipeline was imperative.
