How to use filters with Variant Interpreter

The variant table for Cases in Variant Interpreter allows for filtering the list of variants to only display those matching certain criteria set by the user. For example, all variants can be filtered to display only those resulting from base insertions or deletions (indels) or variants resulting from single nucleotide variations (SNV). These filter sets can be customized and saved for future use and with different sample Cases. The steps below describe how to create and save a filter list and apply the filter to the variants listed for a given sample Case.

1. From the sample Case page, click on the “Apply Variant Filters” button

2. Click on the “check boxes”, “open dials”, etc. to dynamically select filter criteria.

3. “Uncheck” filter criteria to dynamically remove filter criteria.

4. Choose the desired filter criteria. For explanations of each filter type, please see the Variant and Gene Filters page on the Variant Interpreter Online Help page.

5. The filter selections can be saved using the “Save filter as…” link, however this step is not necessary to apply the selected filters.

6. Type the desired name for the filter and click “Save”.

7. Apply the filter by clicking the “Apply” button.

8. After applying the filter, the number of variants of interest should decrease as only those matching the filter settings will now be displayed.

9. To load a previously saved filter, click the “Load Filter” dropdown, select the desired filter, and then click the “Apply” button.

External Links: Variant and Gene Filters help section on Variant Interpreter Online Help page

For any feedback or questions regarding this article (Illumina Knowledge Article #1395), contact Illumina Technical Support [e-mail].