> For the complete documentation index, see [llms.txt](https://docs.finngen.fi/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.finngen.fi/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-plink2-for-unrelated-individuals-only.md).

# 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`.