Fig. 1

PLATO pipeline. This flow chart depicts a typical research pipeline using PLATO. Call rates and minor allele frequency (MAF) can be executed in PLATO and other options for QC are performed elsewhere. A variety of data types can be used as inputs to PLATO, including PLINK files (genotype data), VCF files (sequence data), copy number variant (CNV) data, and exposure data, as well as one or more phenotypes and covariates for adjustment. PLATO offers flexibility for genetic encoding type (additive, dominant, recessive, and codominant are available). Genome-wide association studies (GWAS), gene–gene (G×G) interactions, environment-wide association studies (EWAS), gene–environment (G×E) interactions, phenome-wide association studies (PheWAS), CNV burden analysis, and rare variant (RV) burden analysis are all available in PLATO. Statistical test options currently include logistic, linear, and Firth regression and the likelihood ration test. Finally, Bonferroni, FDR, and permutations can be used to adjust for multiple tests. PLATO output includes an extensive set of statistical results in tab delimited format for ease of use. Included in this Figure is an example of a subset of the results included in PLATO output