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

You can also run GWAS in Sandbox using [plink2](https://www.cog-genomics.org/plink/2.0/). 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`.


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