How to run GWAS using plink2 (for unrelated individuals only)

You can also run GWAS in Sandbox using plink2. There is no FinnGen pipeline for plink2, so this has to be done interactively in the terminal. Because of this, running parallel phenotypes or chromosomes is not possible.

Note: Running GWAS using plink is NOT recommended if you have a large number of samples, phenotypes, or genotypes (for example, running one phenotype in R8 for the whole unrelated set for all imputed genotypes takes >16 hrs).

It is also important to keep in mind that plink2 does not perform mixed models, and thus it should be performed only for unrelated individuals (so not for the whole of FinnGen, for example). You can find relatedness information about R8 samples from /finngen/library-red/finngen_R8/kinship_1.0/data/finngen_R8.kin0.