Running analyses in Sandbox

In this section we will share the following: A guide how you can run your own analyses in the Sandbox.

• How to use the Pipelines tool

• Pipelines is based on Cromwell and WDL

• How to submit a pipeline from the command line (finngen-cli)

• How to run genome-wide association studies (GWAS)

• How to run finemapping pipeline

• How to run LDSC pipeline

• How to run PRS pipeline

• How to calculate PRS weights for FinnGen data

• Sandbox paths and pipeline mappings

• If your pipeline job fails

• Tips on how to find a pipeline job ID

• Managing memory in Sandbox and data filtering tips

Example .wdl and .json files for running these pipelines are in SANDBOX in /finngen/library-green/scripts/. For example, example files for running REGENIE pipeline can be found under /finngen/library-green/scripts/regenie/.