Filter on missingness, Hardy-Weinberg equilibrium, heterozygosity, relatedness and sex checks, then run linear or logistic association tests.

Build scores from the PGS Catalog, a GWAS Catalog search or your own GWAS results, as a simple count or weighted.

Turn genotypes into diplotypes and metabolizer phenotypes, such as CYP2C19 metabolizer status, and use them as variables in your analysis.

Explore genes and variants in your cohort before you test them.

Array, exome and genome data from large biobanks, and VCF or PLINK files from other sources.