2. The Report View Interface

Creating a Clinical Report

This project contains a Yoruban trio from the HapMap project:
  • Mother (NA12938)
  • Father (NA12939)
  • Proband (NA12940)

Two de Novo variants were seeded into the daughter’s BAM file and then SAMtools was used for variant calling on all three family members simultaneously. These variants are flagged and will be included in a clinical report.

To create a report, open the Report View by either:

  • Clicking on the **Plus** in the tool bar and select Report or;
  • Clicking on View > Open > Report
Template Selection

Figure 2-1: Opening the Report View

Adding a New Template

The foundation for a report is a template. Templates are located in your User Data location in a folder called ReportTemplates. Initially, this folder is empty. However, VSReports ships with three example templates to get you started.

  • ACMG Hereditary Gene Panel Report
  • Cancer Gene Panel Report
  • Exome Trio Report Template

First we will create a report template based on the Exome Trio Report Template

  • Click on the Create New Report Template icon **Plus** in the tool bar of the reporting view.
  • Select the Exome Trio Template and name the report template Exome Trio Tutorial and click OK.
Template Selection

Figure 2-2: Report Template Selection

A report template with the entered name will be created in the ReportTemplates folder. It will be accessible in any VarSeq project. By default this template will open in the report view Figure 2-3. If you have multiple templates in the ReportTemplates folder, you can select which to use with the existing template menu located in the tool bar.

Report View

Figure 2-3: selected Report View

Edit the Reference Information and Sample Information fields as in Figure 2-3 to customize the report for the current sample. The values you input are automatically saved on a per sample basis.

Configuring a Clinical Report

From the Gear Menu on the right side of the tool bar, select Configure Report Template.

Report View

Figure 2-4: selected Report View

This dialog contains all the settings which are not expected to change between uses of the template. It contains values such as lab name, log, test description, and gene set Figure 2-5. These fields should be filled out to match the test being run in the lab. The information is saved in the template in the ReportTemplates folder.

Fill in as much or as little as information as desired here. Additionally you can upload a logo to incorporate into a report header. To upload an image to be used in the report template click the Select Image icon.

Report View

Figure 2-5: Report Configuration Dialog

Browse to the VarSeq Reports Tutorial file you downloaded and unzipped and select Golden Helix Header.png to upload the Golden Helix Image to the report header. See Figure 2-6

Report View

Figure 2-6: Report Configuration Dialog

Click OK to close the template configuration dialog and return to the Report View.