4.3. VarSeq Projects

A VarSeq Project is a mechanism for analyzing a set of data from one or more samples using the same workflow from filtering and annotation, to classification and reporting. A template of any project can be created to apply established identical workflow conditions to any group of samples.

4.3.1. Create a New Project

To create a new project, click on Create New Project in the left panel of the Welcome screen.

Create New Project

Select Create New Project

This will open the New Project dialog with a list of existing templates on the left of the screen. Documentation for the template selected in the list is displayed to the right of the list. Selecting the Empty Project template will allow you to start a new project without any Annotations or a Filter Chain (Filter View).

Select a Project Template and choose the Genome Assembly, applicable to your data, from the list. Note, if the template assumes a particular genome assembly, choosing a different genome assembly can result in errors if the template relies on genome assembly specific annotation sources.

Enter in a project name and location to save the project, and click OK.

New Project

The New Project dialog

4.3.2. Download Reference Sequence

If a reference sequence for the genome selected exists on the public data annotations repository, and the reference sequence is not detected in your User Annotations folders, a question dialog will appear asking whether or not the reference sequence should be downloaded.

Download Reference

Download reference sequence question

To prevent this dialog from reappearing for the specific genome, check the “Don’t ask about this genome again” box at the bottom of the dialog.

Otherwise, to download the reference sequence in a background process, click Yes. To not download the reference sequence, click No.

For more information on downloading annotation sources see Download Window.

4.3.3. Open an Existing Project

To open an existing project, click on Open Existing Project in the left panel of the Welcome screen, which will open a browser window, or select the project from the list of recent projects. Note that additional samples can not be added to an existing project.

Existing Project

The Open an Existing Project

4.3.4. Saving a Project as a Template

To save a project as a template to be reused in the future with new data, go to File > Save Project as Template. To change the path for the folder to contain the template click on Browse. To reset the template folder to the default location click Reset.

In the Template Option tab, set the name of the template in the Name box, choosing a unique and identifiable name. Fields are available to capture information about the template and this information will be displayed in the Create New Project window when the template is selected. Fill out as much information as you would like. Full font controls are available by right clicking in any of these text fields. In addition, there is the option to lock the filter chain to prevent modification in any project created from a template.

In the Annotations Options tab, you can choose which the annotation sources will be locked when the template is used or if the latest version should be used.


To tab within a text box:

  • On Mac OSX use <Option> + <Shift> + <Tab>

  • All other operating systems use <Ctrl> + <Tab>

Save As Template Protected

Save Project as Template with the filter chain lock protected (locked)

When all of the information is provided, click Save. Now, a new project can be created rerunning all annotation algorithms, filters, and creating all views with the same or with new data.