Family Based Analysis with Pedigree Information

Workbench allows you to associate pedigree information with your samples, enabling trio or family-based analysis workflows. This guide walks you through the process of adding pedigree data and running workflows with family relationships.

Adding Pedigree Information

Upload Pedigree Files

1. Navigate to the Data page in the left sidebar.

2. Select the connected storage account containing your sequencing data.

3. Click the Add Pedigrees button in the top-right corner.

4. Select one or multiple .ped files (standard pedigree file format).

5. Click Upload to associate the pedigree information with your samples.

Workbench uses a relaxed version of the standard PED format. While the traditional format includes family ID, individual ID, paternal ID, maternal ID, sex, and phenotype information, Workbench allows you to omit sex and phenotype information if these details are not available. The .ped file should not contain a header before uploading else an error will occur.

Pedigree Management

• Cross-Storage Relationships: Family relationships are not storage-scoped. If you have the same samples in multiple storage accounts, the family relationships will be recognized across all accounts.

• Updating Pedigrees: To update existing pedigree information, upload a new PED file with the updated relationships. Workbench will update the relationships accordingly.

Viewing Family Information

Once pedigree information is uploaded, you can:

1. View family groupings on the Samples page.

2. Filter samples by Family ID to see all samples within a particular family.

Running Workflows with Family Data

Running Family-Based Analysis

1. Navigate to the Data page and select your storage account.

2. From the Samples page, you can:

   • Filter by a specific Family ID and select all family members.

   • Manually select individual samples from the table.

3. Click Run Workflow after making your selection.

Workflow Submission Behavior

• Family Grouping: When you select multiple samples belonging to the same family, Workbench will group them together in the workflow submission.

• Automatic Trio Detection: If you select a proband with parents, Workbench will automatically identify and run them as a trio.

• Mixed Selections: If you select samples from different families, each family will be processed as a group, and any remaining samples will be processed as singletons.

Previewing Workflow Runs

1. After selecting samples and clicking Run Workflow, choose the desired workflow and version.

2. Click the eye icon to open the Preview Runs dialog.

3. Review how the samples will be grouped and processed before submitting.

4. Click Submit to start the analysis.

Supported Metadata Fields

The following metadata fields are supported for individual samples:

• Family ID: Identifier for the family group.

• Individual ID: Unique identifier for each sample.

• Paternal ID: ID of the father's sample.

• Maternal ID: ID of the mother's sample.

• Sex (optional): Sex of the individual (1=male, 2=female, 0=unknown).

• Phenotype (optional): Disease status or phenotype (0=missing, 1=unaffected, 2=affected).