Create a Filter Set
- Click on the Filters icon to create and manage filter sets, which you can use on multiple samples. You can duplicate sets, reorder filters within sets or drag and drop filters from set to set.
- Click on the Create icon to create a new filter set.
A pop-up window called Filter set will appear. This window is split into two columns: Available Filters and New Filter set. The available filter sets can be selected by clicking on the green box ("Add") next to each filter’s name. If you select a filter, the filter will move to the other column. By clicking on the "filter name" or on the arrow, a form is displayed where the filter can be edited. Once you have finished editing your new filter set, give it a Name and click on Save filter set.
- You can modify the name of the filter set by clicking on
. In this example, the filter set "Allele Frequencies" will be renamed "Rare Variants":
Applying an existing filter to a variant table
Clicking on the filter icon it opens the Filters menu where filter sets can be managed. To exit this menu, simply press "Esc" on your keyboard.
A drop-down list will show a list of all saved filter sets. Select a filter set from the already existing ones and click on "Add" to add the filter set to the analysis. In order to apply the selected filter set to the analysis select "Apply Filters".
Each of the filters inside a filter set can be switched on and off by clicking on the green/red circles. Active filters have an associated green circle, and inactive filters have an associated red circle. Variants passing the filter are shown in blue, and variants that fail the filter are shown in green and crossed out. In the example below, all filters are active except the Function filter.
Filters can be edited 
or removed 
.
The order of the filters can be changed by moving the mouse on the top of the this icon 
, then dragging the filter and dropping it at the desired position. In the example below, the “Pathogenicity class” filter has been moved to the top position:
Click on 
in order to filter the original results of the variant table. The number of variants that pass the filter is also shown under the variant table. The number of rows of the variant table can be adjusted by selecting: 
. The filters used are shown when placing the cursor on "filtered".
When downloading all the filtered variants from the Variant table in excel format there will be a separate tab called “Filters used” that mentions which filters were used.
Note: If existing filters with Germline Variant Classification rules do not work, you will see an error message returned,
like the following:
In this case you should edit (as shown above) the filter, by adding the rules you would like to have from the available options.
Shared Filters
Users of the same group can now share filters among them. To share a filter with other members of your group, click the Filters link at the navigation bar and then click the share icon on any of the filters you wish to share.
Filters that have been shared among members of the same group appear both on the Filters screen and when filtering a specific analysis. Although a shared filter can be used by anyone in the group, it can only be edited by the user that initially shared the filter. Other group members can still duplicate the filter and edit it.
In the analysis results page, click on the Filters icon, use the drop down list of the search box to select the shared filter of interest, click onto "Add" the shared filter set to the analysis and then click on "Apply Filters".
