Flowchart outlining the quality control and analysis pipeline of this study. SNP data from the control and Old Order Amish populations was used to call CNVs using the PennCNV program. The pedigree structure in the Amish allowed family based calls to be made, and the CNV frequency in the control data allowed us to determine whether the Amish CNV calls were common, rare, or exclusive to the Amish population. We sought to determine CNVs in bipolar individuals, burden in individuals, and CNVs in disease loci. In addition, we utilized the whole genome sequence data to find CNVs and SNPs within the same gene in the same individual.