5. Using a VSWarehouse ReportΒΆ

Warehouse can be used to store sample report data. This allows you to view previous reports, as well as query across the variants that have been included in the report findings. Now that we have finished filtering the variants we will create a report with the filtered variants and upload it to VSWarehouse.

  1. First, we will open a VSWarehouse hosted report template. Open the manage VSWarehouse dialog and navigate to the Reports tab Figure5-1

    Reports tab of the VSWarehouse manage dialog

    Figure 5-1: Open the reports tab in the VSWarehouse management dialog.

    Select the Cancer Panel Report and click Open. This will open that report in a new VSWarehouse tab in your VarSeq project.

  2. The next step will be to add sources required by the report that are missing from the project. These sources are used to autofill the data in the report. Click the red triangle in the upper right hand corner of the report view to view the current errors. The menu should display that two required sources are missing, and four optional sources are missing. Click each of the messages and add the missing annotations to your project.

    Add missing report sources

    Figure 5-2: The report is missing required OncoMD annotations, and optional OMIM sources.

    Adding these premium annotations will allow information from these annotations to be included in the report.

  3. While the annotations are running you can start to fill out the report template with some basic sample information.

    Report with patient and sample information

    Figure 5-3: Report with the patient and physician information.

    The values that are placed in the form are used to render the report once it has been filled out. Additionally these are saved on the warehouse where they are aggregated across all of the reports that have been created using this template.

  4. After the patient and physician information has been filled out the next step is to select the variants that will be included in the report using Variant Sets. To add a variant set click the square icon in the variant table view.

    Report with patient and sample information

    Figure 5-4: Adding a variant set to the variant table

    This will open the Create Variant Set dialog. Name the record set Primary Findings change the Initials to PF and click OK. Add an additional variant set named Incidental Findings with the initials IN colored green, following the same steps.

    Report with patient and sample information

    Figure 5-5: Naming the new variant set

    This will create two new flags fields. Add the top two variants to the Incidental Findings flags by clicking the colored square for each record under the IN field. Add the last variant to the Primary Findings category.

    Flagged Variants

    Figure 5-6: Flagging the filtered Variants

    Finally, select the variants sets that correspond to the Primary and Incidental section in the reports view. This will take the information from the selected variants and fill it in the report.

    Selecting Record Sets

    Figure 5-7: Selecting the report record sets

  5. Next check the signoff checkbox. Then click the render report button at the top of the report view. This will open a web view prompting you to log into VSWarehouse. After you log in the rendered html report will load from the VSWarehouse.

    Render the Report

    Figure 5-8: Click the render button to load the rendered report from VSWarehouse.

    The report has now been saved on the warehouse. All of the samples and the variants in their findings can be viewed and queried from the warehouse. Additionally the variant set in the report can be used as an annotation source.

  6. To add the variants from the findings section as an annotation source open the Manage VSWarehouse Dialog. Navigate to the annotations tab and find the Cancer Panel Report - Primary Findings source.

    Report Annotation

    Figure 5-9: Adding the Primary Findings from the report

    Adding this source will add the primary findings from the source that was just uploaded to the warehouse as an annotation source. Scrolling all the way to the right of the table you will see the variant included in the Primary Findings appear as an annotated variant.