Create a user-defined filter chain

You can create a user-defined filter chain to refine analysis results in Ion Reporter™ Software. A filter chain is a set of filters that can be applied to the variants identified in an analysis that are used to narrow the analysis results to only the variants of interest. After you create a user-defined filter chain, you can associate the filter chain with an Ion Reporter™ Software analysis workflow when you create or edit the analysis workflow. You can also apply the filter chain to analysis results.

IMPORTANT! If using a single filter with a NOT operator, do not use a parenthesis. If parenthesis is used, the filter chain can be saved but an error occurs when applying the filter chain in analyses results. For example, use NOT Filtered Coverage instead of NOT (Filtered Coverage).

To create a user-defined filter chain, use one of the following procedures to get started.

Option	Description
Workflow Presets	In the Workflows tab, click Presets. Click Create PresetFilter Chain.
Analysis Results	In the Analysis tab, click Overview. Click the link of an analysis of interest. The Analysis Results screen appears. In the right pane, in the Filter Chains section, click (New).

In the Create Filter Chain dialog box, enter a name and, optionally, a description.
In Reference, select the reference type to use for this filter chain.
Apply filters to the filter chain.

The available filters depend on the selected reference type.
1. From the Choose Filter list, select one or more filters to add.
  
  For more information, see Annotation source filters and Data type filters.
2. If more settings are available, set the appropriate conditions for the selected filter.
  
  For more information, see Annotation source filters.
3. Click Add to add the filter to the Selected Filters list.
4. Repeat to add more filters.
  
  The filter count is incremented (for example, --2) as you add more filters, and the selected filters are added to the FilterChain Query in order.
(Optional) Use Update to add a second instance of an existing filter, or to configure and replace the last filter instance in the list without changing the filter count.
Click Save.

The filter chain is available to be associated as the default filter chain when an analysis workflow is created, or to be used to change an existing default filter chain. For more information, see Add a filter chain to an analysis workflow and Change the default filter chain for an analysis workflow.

The filter chain can also be applied to analysis results or to a visualization. For more information, see Apply a filter chain to analysis results and Use filter chains to change analysis results.