> 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/which-tools-are-available/untitled.md). # Custom GWAS tools ### Trade-offs of different methods We provide a number of methods that enable you to run GWAS for your custom endpoint(s). This table describes the trade-offs of different methods. All methods use [REGENIE](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-regenie.md). There are also instructions to use [SAIGE](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-saige.md) available, but since DF7 we have moved to use REGENIE, and SAIGE has not been supported similarly since. #### The fastest way to get results calculated The easiest way to get results calculated and out of the sandbox is to use the methods in the first 2 rows - these methods enable the summary statistics to be automatically put into the green bucket and [user.results pheweb browser](https://userresults.finngen.fi). If you want to browse your results outside of sandbox, the 2 lower methods require that you request to have results downloaded, which can take more time especially off-hours Helsinki time. These methods also require a bit more coding skills. Using these methods, however, you are able to modify some parameters in your job, e.g. covariates. | Category | Methods Available | Running time | Cost | When to use | How to launch | Viewing your results | Pros | Cons | | ----------- | -------------------------------- | ---------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------- | | Custom-GWAS | Custom GWAS Command-line version | Usually <24 hours until results in userresults.finngen.fi PheWeb | 20–50€ per GWAS depending on availability in Google Cloud and increases with each DF. Charged to sandbox account | List of FinnGen IDs and case/control status in plink format (can be generated programmatically) | From terminal: `finngen-cli request-gwas --help` | Results automatically moved to userresults.finngen.fi (outside sandbox). Available for download and further analysis. Whole process \~24 hours | No coding required; results automatically available in PheWeb; fine-mapping can be requested from support | Cannot modify covariates (age, sex, genotyping batch, PC1–10 fixed); only releases 7 onwards | | Pipelines | Command line | \~8 hours for DF11 | Same as above | Running >5 GWAS; need different covariates or private results; additional analysis steps (e.g., subset summary stats) | From terminal: `finngen-cli request-workflow --help` | View and interpret results inside sandbox using R/Python (libraries preinstalled; can request more). To view outside sandbox, download data | Can modify covariates; can run multiple phenotypes in one job | No automated import to PheWeb; requires coding skills (editing input files) | | Pipelines | Standard pipelines | \~8 hours for DF11 | Same as above | Pipeline scalability: submit multiple phenotypes simultaneously using phenotype list | From sandbox menu: Applications > Pipelines > New job from Templates | Same as above | Same as command line pipelines | Same as command line pipelines | In the subsection below we describe the method you can use to have your results visible in userresults.finngen.fi: * [Custom GWAS commandline (CLI) tool](/working-in-the-sandbox/which-tools-are-available/untitled/custom-gwas-command-line-cli-tool.md) And in the subsections here we describe the two other methods you can use to run GWAS for your custom endpoint: * [REGENIE pipelines using command line](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-regenie.md) * H[ow to use standard pipelines](/working-in-the-sandbox/running-analyses-in-sandbox/pipelines-tool-instructions/how-to-use-the-pipelines-area.md#submit-a-standard-job) However you can learn more about other additional methods under ["How to create a user-defined endpoint"](/finngen-data-specifics/endpoints/link-to-how-to-make-a-user-defined-endpoint.md). ### Upstream analysis Before entering GWAS consider investigating your phenotype and genotype cohorts. For further instructions see: * [General workflows for the most common analyses](/working-in-the-sandbox/general-workflows-for-the-most-common-analyses.md) researchers are conducting with FinnGen data in FinnGen Sandbox * [Trajectory Visualization tool](/working-in-the-sandbox/which-tools-are-available/trajectory-visualization-tool-tvt.md) * [Cohort Operations tool](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co.md) ### Downstream analysis After custom GWAS is conducted you may consider further downstream analyses like * [How to conduct Finemapping](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-finemapping-pipeline.md) to assign a probability that each significant variant at a locus is the causal variant. More [background reading about Finemapping](/background-reading/finemapping.md). * [Multiple Manhattan Plot](/working-outside-the-sandbox/multiple-manhattan-plot-mmp.md) to compare several GWAS summary statistics.