Genomic screening with ClinVar (Azure tutorial)

Allie Cliffe
  • Updated

If you're interested in using Terra on Azure, please email terra-enterprise@broadinstitute.org.

1. Clone the template workspace

1.1. Click on the three-dot menu at the top-right of the workspace and select Clone.

M42-ClinVar-screening_step-1.1.png

1.2. Fill in a Workspace name. In this example, I’ve added my initials and the date so it’s easy to identify. Select your Terra Billing project and click the CLONE WORKSPACE button.

M42-Screening-with-ClinVar_step-1.2_Clone-workspace-form.png

1.3. Your cloned workspace will take a few minutes to create.

GenomicScreening_1.3-loading-clone.png

2. Examine the workspace data table

2.1. Navigate to your cloned workspace (Main menu > Workspaces > Genomic Screening with ClinVar) and click on the DATA tab. 

M42-Screening-with-ClinVar_step-2.1_Click-data-tab.png

2.2. The workspace comes with a data table called cohorts. Click on the name to examine the table.

M42-Screening-with-ClinVar_step-2.2_Cohorts-table.png
2.3. This table contains one row and five columns of data.

M42-Screening-with-ClinVar_step-2.3_Cohorts-data-table.png

The bed_file and input_vcfs columns contain links to the files in the Terra workspace’s Azure storage container that will be used as inputs for the VariantAnnotation workflow.

3. Run the VariantAnnotation workflow

Workflows are orchestrated in Terra by the workflows application - Cromwell. When you are in a new workspace, you will need to launch Cromwell. Note that you only need to do this once, the first time you set up or run a workflow in the workspace.

3.1. Go to the Workflows tab.

3.2. Click the blue Launch Workflows App button.

GenomicScreening-LaunchWF-3.2.png

GenomicScreening-2.3.1-symbol.pngThe Workflows app may take between 5-15 minutes to launch.

When workflows are ready

After a few minutes, you will see the workflows menu on the left-hand side and the VariantAnnotation workflow from the original workspace in the center under Workflows in this workspace. 

M42-Screening-with-ClinVar_step-3.2_Screenshot-of-VariantAnnotations-card.png

3.3. Click the blue Configure button for the VariantAnnotation workflow.

3.4. The data table should already be set to the cohorts table. If it is not already selected, choose it from the dropdown menu. Check the box to select the only row in the table.

M42-Screening-with-ClinVar_step-3.4_Configuration-form.png

3.5. The Inputs and Outputs have already been configured for you. You can click on the Input tab to see which workflow attribute (input table column) holds each variable.

Inputs configuration

M42-Screening-with-ClinVar_step-3.5_Configure-inputs.png

Clicking the outputs tab lists the workflow outputs (genes annotation and position annotation JSONs, a variant report PDF and a variant table TSV) and where output data will be written back to the table (in the Output name column). 

Outputs configuration

M42-Screening-with-ClinVar_step-3.5_Configured-outputs.png

3.6. When you’re ready to run the workflow, click the blue SUBMIT button. You can add a comment for this submission if you wish, then click SUBMIT again.

M42-Screening-with-ClinVar_step-3.6_Send-submission-form.png

What to expect 

The first time you run a workflow in your workspace, Cromwell will take some time to launch. The workflow will submit automatically once Cromwell is up and running and you will be redirected to the Submission details page.

M42-Screening-with-ClinVar_step-3.8_Submission-details-when-running.png

The Submission history shows an overview of the run at any time. 

M42-Screening-with-ClinVar_step-3.8_Submission-history-workflow-running.png

3.9. Once the submission is complete, you will see the status change to Success. From the submission history, you can click on the submission name for more details including log files for troubleshooting.

M42-Screening-with-ClinVar_step-3.9_Submission-history-successful-run.png

4. Find/explore results

4.1. Click on the DATA tab to examine the cohorts table once more.

M42-Screning-with-ClinVar_step-4.1_Click-on-data-tab.png

4.2. Click to open the cohorts table and scroll to the right to see the newly generated output files that have been added to the table in four new columns.

M42-Screening-with-ClinVar_step-4.2_New-columns-for-outputs-in-cohorts-table.png

Accessing output files

4.3. Clicking on the link in the genes_annotation_json column will expose where the file is stored in your workspace cloud storage and allow you to download the output file to local storage.

M420Screening-with-ClinVar_step-4.3_Output-files-in-workspace-storage.png

M42-Screening-with-ClinVar_step-4.3_Download-outputs-modal.png

 

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