2. New Project WorkflowΒΆ

This tutorial walks the user through an ACMG workflow from blank template through to report. First, a new, blank project will be created, the VCF file imported, the variants filtered, and the ACMG Classifier run on the selected variants. This will lead to some example case variants and finally a report to highlight the results.

This tutorial was accompanied by a VCF file contained in a ZIP file. Before starting, download the ZIP file, and extract the contents to a convenient location.

This tutorial begins by opening up a new instance of VarSeq and creating a new project with the GRCh37 Genome Assembly and Empty Project template. The image below shows these options and labels this project: ACMG Tutorial Example.

New Project 1

Figure 2-1: New project dialog.

Selecting OK brings you to the next screen that directs the user to import variants. Select Add Files, navigate to the location of the extracted ZIP file, and add select the VCF file. The default selections can be kept, and the import completed by selecting Next three times and then Finished.

Import variant wizard dialog

Figure 2-2: Import variants wizard opening screen.

Import variants wizard options

Figure 2-3: Import variants wizard workflow.

At this point we have a blank template project with 1 sample imported consisting of 30,294 variants, so the next step is to filter the variants down to a smaller number of applicable variants for further examination.