Managing Samples¶

Once your files have been uploaded and processed, they appear in your sample list. This page covers how to view, organize, and manage your samples.

Browsing your data¶

Navigate to the Samples tab. The Samples page offers two ways to browse your data:

Browse by Projects¶

View your data organized by project. Each project groups related samples together, making it easy to find all samples for a specific study, patient cohort, or collaboration. Click a project to see its samples.

Browse by Samples¶

View all your samples as cards across all projects. Each card displays:

• Sample name: The file name or a custom name you assigned.
• Row count: The number of data rows (variants or records) in the sample.
• Project: The project the sample belongs to.
• Owner: The user who owns the sample.
• Status: Processing status (e.g., Ready, Processing, Error).

Click on any sample to open it in the Table View for exploration and analysis.

Sample Metadata¶

Each sample has associated metadata that you can view:

• Sample name: The sample name used during upload.
• Total variants/rows: The number of records loaded into the database.
• Created timestamp: The date and time the sample was created.
• Assembly: Whether the sample is GRCh38 or GRCh37.
• Sample type: The type of sample (e.g., WES, WGS).
• Status: The current status of the sample (e.g., Ready, Processing, Error).
• Project assignment: Which project the sample belongs to, if any.
• Clinical notes: Any clinical notes associated with the sample in plain text.
• Phenotype terms: Any phenotype terms associated with the sample.

Deleting Samples¶

To delete a sample:

1. Navigate to the Samples tab.
2. Locate the sample you want to delete.
3. Click the Delete action (trash icon or delete button) for that sample.
4. Confirm the deletion in the dialog that appears.

Assigning Samples to Projects¶

Samples can be organized into projects for collaboration and grouping:

1. Navigate to the Browse by Projects tab in the Samples page.
2. Click on +New Project button on top right to create a new project, or select an existing project.
3. Click on Add Sample button on the top right to add/upload a sample to the project.
4. Refresh the page and confirm the assignment.

Once assigned, the sample is visible to all collaborators on that project according to their role.

Managing projects¶

Projects are used to organize and collaborate on samples. You can create projects to group related samples and share them with collaborators.

Adding members¶

1. Open a project and click the Settings icon in the top right.
2. Enter the email address of the person you want to add. The email must belong to an existing AIVA account.
3. Confirm to add them as a project member.

Once added, members can see all samples assigned to the project according to their role.

Deleting a project¶

1. Open the project and click the Settings icon in the top right.
2. Select Delete Project.
3. Type the project name to confirm.
4. Choose Delete Project Only to keep the samples, or Delete Project and All Samples to remove everything.

Tips¶

• Name your samples meaningfully: Use patient IDs, experiment names, or descriptive labels so you can quickly find samples later.
• Clean up old samples: Delete samples you no longer need to keep your workspace organized and free up storage slots. BAM files from secondary analysis pipelines also count toward your slot limit.