The CHARGE Analysis Committee developed a set of general plans as guidelines for all working groups. The issues include quality control of genotype data, decisions about what results to share across cohorts, formats for sharing data, strand alignments, coding of alleles, choice of covariates for adjustments, detection of and correction for population structure, within-study phenotype analysis plans, between-study meta-analysis methods, and the importance of written analysis plans prior to sharing the results. The goal was to provide a flexible plan that could be adapted or adopted by working groups. For each stage in the analysis, there are several valid options available, and some are summarized briefly.
