7. Exploring VSWarehouseΒΆ

From the VSWarehouse web interface you can view the samples, variants, assessment catalogs, and reports that have been uploaded to the VSWarehouse. Each of these categories can be queried and exported from using the same Query and Result interfaces.

  1. Open the web browser of your choice and log into the VSWarehouse. This will open the VSWarehouse homepage, which is divided into four sections. One for each category of data stored on the warehouse.

    VSWarehouse home

    Figure 7-1: VSWarehouse home screen

    In the project section, select the Cancer Gene Panel. This will open the VSWarehouse project that corresponds to the VarSeq project was previously uploaded.

  2. To find other rare variants in the BRAF gene opened the query interface by selecting Query at the top of the page. This will open the query interface where you can construct filters based on the fields in the data.

    VSWarehouse query

    Figure 7-2: VSWarehouse query screen

    Next add a filter in the Allele Counts section for the Allele Frequency with an upper bound of 0.01, and uncheck include missings.

    Adding an allele counts query

    Figure 7-3: VSWarehouse query screen

    This will filter to rare variants that occur in less than 1 percent of the samples that been added to this project. Next switch to the RefSeq Genes 105v2, NCBI section to add a filter for the Gene Names equal to BRAF. Finally add a filter for the RefSeq Genes 105v2, NCBI field Effect (Combined) equal to Missense.

    Adding the Effect (Combined) filter

    Figure 7-4: Add the Effect (combined) filter equal to Missense.

    This should reduce the number of variants to 3. To view the variants click Results at the top of the page.

  3. The results page will display the three records that pass the filters. Change the visible fields by selecting Change Columns. This will display the published columns that are available on the left and the current visible columns on the right.

    Changing column visibility

    Figure 7-4: Changing the columns visible in the results

    Add the Allele Frequencies field from the Allele Counts category, as well as the Drug, Generic Name and Response Rate fields from the OncoMD Drugs Targeting Mutation category.

  4. Next select Export at the top of the screen to save the results. Select Excel as the file type and under Select Samples click Unselect All. This will remove the sample fields from the output.

    Export results

    Figure 7-4: Export the filtered results

    Clicking Export will start a job to perform the export. Click View Task to see the status of the job, and to download the results after it has completed. You can then open the file in Excel shown in the VSWarehouse results.