This repository contains files that provide an outline for conducting methylation data quality control and performing either single genetic ancestry, or multi-ancestry epigenome-wide association studies (EWAS). The phenotype used as an example in these files is BMI, but this can be substituted with any phenotype or trait of interest. Additionally, the multi-ancestry script can be modified to stratify on any variable (race/ethnicity, biological sex, case/control, etc.). These scripts are not a part of a formal package, so must be downloaded locally, by the web address, or copy and pasted.