Downstream analyses after the Atlas cohorts are created
Now that the cases and controls cohorts are created, we may proceed to downstream analyses like custom GWAS analysis on these cohorts using the custom GWAS GUI tool or launch the same custom GWAS from the Cohort Operations.
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.
Tools designed for exploring cohorts
Cohort Operations tool (can read a cohort directly from Atlas)
Trajectory Visualization tool (can read a cohort directly from Atlas)
Downstream analyses after the Atlas cohorts are created
Exporting an Atlas cohort for other tools
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 Binary mode (same analysis as also available with Custom GWAS GUI and Custom GWAS with Cohort Operations)
Custom GWAS GUI and CLI tools will export the summary data to the Green library and the results are automatically loaded to FinnGen User Results in the PheWeb format.
Further analyses
Genome-wide association studies (GWAS)
GWAS using REGENIE can be run from pipelines if e.g. input parameters need to be modified. Otherwise, Custom GWAS tools are easier to use.
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