Workflows, scripts and containers for data analysis

This section contains example scripts and code chunks as well as entire analysis workflows to get you up-and-running with analysis in the Research Environment.

Most of these scripts and workflows are present in the Research Environment under the folder: /gel_data_resources/example_scripts. Check out the Getting workflow support page if you run into any difficulties. Many of these scripts and workflows require you to build a cohort as a startpoint, you can learn more about this in our tutorial

Feel free to get in contact with us if you would like further assistance in writing your own scripts or if you have a script or workflow of your own that you would like to share with the research community!

Workflows

Association testing

• Aggregate Variant Testing (AVT) workflow performs rare variant association analysis
• GWAS pipeline performs genome-wide common variant association analysis

Variant screening

• Small Variant workflow extracts and annotates variants within a query gene(s)
• Structural Variant workflow extracts CNVs and SVs within a query regions defined by gene(s) or coordinates

Scripts

• Extract variants by coordinate
• Somatic SVs and CNVs for a specific gene
• Cancer survival analysis
• Variant Effect Predictor annotation

Containers

Container repositories

• Docker Hub
• Quay.io

See the documentation on Using containers within the Research Environment.

Public genome analysis software in the Research Environment

A full list of available software can be shown within the Research Environment by typing module avail once connected to the HPC.

Our future plans

You can keep up-to-date with our plans for workflows and scripts in the RE, give us feedback on those plans and make suggestions using our Productboard roadmap.