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Apply Variant Filters

Variant filters provide options for applying combinations of inclusion and exclusion filters to the data in a case. Filter criteria vary depending on the selected variant categories. Only filters that are relevant to all variant types within a filter group are listed.

Test definitions specify the default filters applied to the data. Each filter combination resides on a different tab in the variant grid. You can create new filter tabs in the grid for as many additional case-specific views as necessary.

For more information about filter options, see Variant Filters and Filtering Logic.

ClosedCreate Filter Views for Tests

When you configure a new test, you can create saved filter combinations and include them in the test. TruSight Software automatically populates tabs in the variant grid with the filter combinations applied.

1. In the Reports section of the Test Management page, select Create New Filter.
2. Add a descriptive name for the filter.
3. To specify a list of genes to include, select Genes field and then do any of the following:
• Select Auto apply genes from phenotypes. TruSight Software automatically generates a list of genes associated with specified phenotypes.
• Select the Gene Lists field, and then select one or more gene lists. For information about adding gene lists, see Gene List Files.
• Select Additional Genes, and then enter one or more gene names, separated by a comma or new line.
4. Select the Variant Category field and then select one or more variant types.
5. Add category filters.
  1. Select Add Criteria and then select a filter category.
  2. Select the filter category field and then select or enter the filter criteria.
  3. Choose whether to include or exclude variants that match the criteria. The default is Include.
6. [Optional] Select Create New Filter Group to add a filter group. Filter groups are applied in addition to the base filter and independent of other filter groups.
ClosedApply Saved Filter Views to Tests

Add saved filter combinations to tests. TruSight Software automatically populates separate tabs in the variant grid for each filter combination applied.

1. In the Reports section of the Test Management page, select the Interpretation Filters drop-down menu.
2. Select one or more filter views. To review the details of a filter in the list, select View.
ClosedClone a Test Filter View to a New Filter

Cloning a filter view uses an existing filter combination as the basis for a new filter.

1. In the Reports section of the Test Management page, select the Interpretation Filters drop-down menu.
2. Select View for the filter you want to copy.
3. Enter a unique name for the filter.
4. Modify the filters as needed, and then select Save as New Filter.
ClosedDelete a Test Filter

Delete unused filters from the filter list. Filters associated with active or retired tests cannot be deleted.

1. In the Reports section of the Test Management page, select the Interpretation Filters drop-down menu.
2. To review the details of a filter in the list, select View
3. Select Delete . The delete option is disabled for filters in use.
ClosedCreate New Filters in the Variant Grid

Configure and modify case-specific filter views in new or unlocked variant grid tabs. Default filter tabs, indicated by a lock icon, cannot be altered or deleted.

1. Create a new tab using one of the following methods:
• To create a new view that displays all variants, select New View.
• To copy an existing view with filters applied, select the tab drop-down arrow and then select Duplicate View.
2. [Optional] Double-click the tab label and enter a new name.
3. Select Show Filters.
4. To specify a list of genes, select the Genes field and then do any of the following.
• Select the Gene Lists field, and then select one or more gene lists. For information about adding gene lists, see Gene List Files.
• In the Additional Genes field, enter one or more gene names, separated by a comma or new line.
5. To add a list of genes based on associated phenotypes, select the Genes field and then do as follows.
  1. Select Include genes from phenotypes.
  2. Add one or more phenotypes in the Phenotypes field.
  3. [Optional] Modify the search parameters. The default parameters are specified in the test configuration.
  4. [Optional] Refine the phenotypes list to include or exclude genes associated with related terms.
  5. Select Apply.
6. Select the Variant Category field and then select one or more variant types.
7. Add category filters.
  1. Select Add Criteria and then select a filter category.
  2. Select the filter category field and then select or enter the filter criteria.
  3. Choose whether to include or exclude variants that match the criteria. The default is Include.
8. [Optional] Select Create New Filter Group to add a filter group. Filter groups are applied in addition to the base filter and independent of other filter groups.
9. To remove a filter view, delete the tab.

Default tabs are indicated by a lock icon and cannot be deleted.

ClosedExport Filtered Variants

Export a list of variants and variant data to a tab-delimited file.

NOTE

The maximum number of exported variants in a list is 7500. If the list exceeds the maximum, only the first 7500 results are included in the exported file.

1. Create a filter view that includes the variants to export.
2. Select the tab drop-down arrow and then select Export.