1. Frequently Asked Questions

1. How do I add a user to a project?

Users can be granted access to projects from Settings & More in the left menu. Once selected, click on Settings and then click Project Members (or Collection Members) to manage members. See the Settings & More section in Projects for more information. Only users with Admin access or above can add or modify members.

2. Does Mosaic support direct messaging between collaborators?

No. In conversations, if you use @USER, that specific user will be notified (both within Mosaic and via email) that they have been mentioned in a conversation. This message is still visible to all other people with access to the conversation. Mosaic does not support any private messaging between users.

3. Will applying a template to an existing project overwrite any information in the project, for example comments in conversations?

No. For example, if the template contains a conversation with the same name as a conversation that already exists in a project, applying the template will see the conversation already exists and leave it alone. It will not create a duplicate conversation. See Templates for more.

4. What is the difference between a project and a collection?

A project holds the data for a single case — for example, an individual or a family trio. A collection is a group of projects managed together as a cohort. Collections let you view attributes and query variants across all of their projects at once. See Projects and Collections. A project can belong to more than one collection.

5. What is the difference between Public, Protected, and Private projects?

Public projects are visible and accessible to anyone. Protected projects require access to be granted, but are listed so users can find them and request access. Private projects also require access to be granted, but are hidden so they cannot be found or requested. These privacy levels are set when a project is created and can be changed later in the project settings. See Creating Projects and Collections.

6. Why does the variants table show fewer variants than I expected?

By default, the Variants table shows a computationally prioritized subset rather than every variant in the data, filtered on factors such as population frequency, predicted impact, known pathogenicity, and phenotype. The Why aren't there more? control above the table explains the prioritization currently in effect, and adjusting the filters changes which variants are loaded.

7. Should I create attributes directly in my case projects?

Generally no. Attributes that need to be shared or compared across projects should be created as public attributes in a dedicated Public Attributes project or in a template, not ad hoc in individual case projects. This keeps attributes consistent across your data. See Project Attributes.

8. How do I create a template?

Templates are ordinary projects with a flag that designates them as a template. This flag can only be set using the API, so please contact the Frameshift team to have a template created. Once created, a template is edited like any other project. See Templates.

9. How will I know when there are new variants to review for a case?

Set up a Subscription to the relevant collection so that ClinVar reanalysis tasks appear on your Tasks page and you are notified within Mosaic; an email is also sent to the addresses associated with the reanalysis process. See Tasks and ClinVar Reanalysis.

10. Can I do things in bulk or automate repetitive work?

Yes. Most actions available in the interface can also be performed through the Mosaic API, which is well suited to repetitive or large-scale operations. A public Python client is available. See API.

11. Can I add custom annotations to my project variants?

Yes. Although it will require a bit of work with our bioinformatics team. Just contact the Frameshift team and we'll guide you through the process.

Anything else?

If you have any questions on Mosaic, please contact the Frameshift team.