# Downstream analyses after the Atlas cohorts are created Now that the[ cases](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/how-to-define-a-simple-icd-case-control-cohort-in-atlas/define-a-simple-icd-case-cohort-in-atlas.md) and [controls](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas/how-to-define-a-simple-icd-case-control-cohort-in-atlas/define-a-simple-icd-control-cohort-in-atlas.md) cohorts are created, we may proceed to downstream analyses like custom GWAS analysis on these cohorts using the same custom GWAS from the [Cohort Operations](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co/launch-custom-gwas-with-co.md). It is highly recommended to explore the cohorts before conducting heavy computing like GWAS according to instructions in [General Workflows for the most common analyses](/working-in-the-sandbox/general-workflows-for-the-most-common-analyses.md). ### Tools designed for exploring cohorts * [Cohort Characterizations tool in Atlas](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/cohort-characterizations-in-atlas.md) * [Improving cohorts using Cohort Characterizations tool in Atlas](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/cohort-characterizations-in-atlas/improving-cohorts-using-cohort-characterizations-tool.md) * [Cohort Operations tool](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co.md) (can read a cohort directly from Atlas) * [Trajectory Visualization tool](/working-in-the-sandbox/which-tools-are-available/trajectory-visualization-tool-tvt.md) (can read a cohort directly from Atlas) ### Downstream analyses after the Atlas cohorts are created * [Cohorts diagnosis and drugs pathways (Sunburst plot) with Atlas](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/cohort-pathways.md) * [Explore medical code (diagnoses, drugs, operations, etc.) enrichments with Cohort Operations](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co/explore-code-and-endpoint-enrichments-with-co.md) * [Explore code overlaps between control and case cohorts using Cohort Operations tool](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co/understanding-phenotypic-overlaps-using-co.md) * [Compare custom endpoints to FinnGen endpoints with Cohort Operations](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co/compare-custom-endpoint-to-finngen-endpoint-with-co.md) * [Launch Custom GWAS with Cohort Operations](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co/launch-custom-gwas-with-co.md) ### Exporting an Atlas cohort for other tools * [exporting the cohorts from Atlas](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co/export-finngen-ids-using-co.md) Exported Atlas cohorts are text files that can be read in and further modified for other tools using e.g. R, Python, or Unix. After being modified to the correct input format cohorts initially built with Atlas can be used in any tool available in FinnGen Sandbox. * [Custom GWAS CLI tool](/working-in-the-sandbox/which-tools-are-available/untitled/custom-gwas-command-line-cli-tool.md) * [Custom GWAS CLI Binary mode](/working-in-the-sandbox/which-tools-are-available/untitled/custom-gwas-command-line-cli-tool/custom-gwas-cli-binary-mode.md) (same analysis as also available with Custom GWAS in Cohort Operations) * [Custom GWAS CLI Quantitative mode](/working-in-the-sandbox/which-tools-are-available/untitled/custom-gwas-command-line-cli-tool/custom-gwas-cli-quantitative-mode.md) Custom GWAS CLI tools will export the summary data to the Green library and the results are automatically loaded to [FinnGen User Results](https://userresults.finngen.fi/) in the [PheWeb](/working-outside-the-sandbox/link-to-how-to-use-pheweb.md) format. #### Further analyses * [Running analyses in Sandbox](/working-in-the-sandbox/running-analyses-in-sandbox.md) * [Pipelines tool](/working-in-the-sandbox/running-analyses-in-sandbox/pipelines-tool-instructions/how-to-use-the-pipelines-area.md) * [Genome-wide association studies (GWAS)](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas.md) * [GWAS using REGENIE](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-regenie.md) can be run from pipelines if e.g. input parameters need to be modified. Otherwise, Custom GWAS tools are easier to use. * [Conditional analysis](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/conditional-analysis.md) * [GWAS with SAIGE](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-saige.md) * [Adding new covariates in GWAS using REGENIE and SAIGE](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/adding-new-covariates-in-gwas-using-regenie-and-saige.md) * [Plink2](/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) * [GWAS using GATE (survival models)](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-gate-survival-models.md) * [Finemapping pipeline](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-finemapping-pipeline.md) * [LDSC pipeline](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-ldsc-pipeline.md) * [PRS pipeline](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-prs.md) --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. 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