3.6.5. VSReport View

If licensed, VarSeq includes a feature to create Clinical Reports. This feature enables users to create custom export formats to return to physicians or integrate with legacy systems. The most common output format is HTML, which can be easily saved as a PDF in VarSeq. However, other formats such as XML, JSON, and CSV can be targeted for output.

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, VarSeq ships with three example templates to get you started. To add an example template to the folder, click on the Create New Report Template icon **Plus** in the toolbar of the reporting view. You will be prompted to select a starting template and to enter a name for your template. After clicking OK, a template with the entered name will be located in the ReportTemplates folder. It will be accessible in any VarSeq project. By default this template will open in the report view. If you have multiple templates in the ReportTemplates folder, you can select which to use with the existing template menu located in the toolbar.

Template Selection

Report Template Selection

Report View

Selected Report View

Creating a Report

To create a report, open the Report View and select a template from the existing template menu.

From the Gear Menu on the right side of the toolbar, select Configure Report Template. 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 (Cancer Template). 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.

Report View

Report Configuration Dialog

After closing the template configuration dialog, return to the Report View. Edit the fields as necessary to customize the report for the current sample. The values you input are automatically saved on a per sample basis.

The Genetic and Incidental Variant sections require that a variant set be present in the project. Select the appropriate variant set from the selection box and a list of variants will be added to the form. In the default template, variants have two user settable fields:

  • Classification: This field is used to set the variant’s classification category. If an assessment database has been used as an annotation source, the classification will be set to the value used in the database. This value can always be reset by the user in the report tab. Note that changing this classification in the report tab will not be reflected in the assessment database.

  • Interpretation: The interpretation section is used to describe the variant. The initial text is pulled from up to three sources – RefSeq Genes (sequence ontology), NHLBI ESP6500 (variant frequency), and OMIM (textual description). The links used in this section are used to generate the references found at the bottom of the report.

Once you are satisfied with the selections, click the Sync icon in the toolbar to render the report in HTML. The rendered report will automatically open in a Web Browser tab. See VSReports for example reports.

Click on the Export icon **Export** to export the report as a PDF document. You will be prompted to enter the name of the output file. You can additionally open the containing folder (to view the HTML file directly) or open the HTML page in an external browser.

Adding Variants to the Report

To add variants to the report, click on the Record Sets icon in the Table View toolbar and click on Create Variant Set…. See Record Sets for more information.

Then from the Select a Variant Set (Create from Table Toolbar) option in the report template select your created variant set(s).

Adding Variants

Adding Groups of Variants to Report

Customizing Reports

Reports are fully customizable and Golden Helix is happy to offer customization services. For more information contact your account manager.

Users with JavaScript development experience can extensively modify templates to customize their own reports, see VSReports Templates for further details.

Reports Hosted on VSWarehouse Server

With VSWarehouse, report templates can be centrally managed, versioned and most importantly can save and index the sample and variant level report data. See Warehouse Hosted Reports for further information.