Create a COSMIC, ClinVar, MAF, and Variant Effect filter chain

You can create a custom filter chain that includes both annotation source filters and Ion Reporter™ Software variant data type filters. This procedure shows how to create a COSMIC, ClinVar, Minor Allele Frequency (MAF), and Variant Effect filter chain.

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).

  1. In the Workflows tab, click Presets.
  2. Click Create Preset > Filter Chain.
  3. In the Create Filter Chain dialog box, enter a name and, optionally, a description.
  4. In the Choose Filter list, select COSMIC.
    1. Select the top checkbox to select all values.
    2. Click Set.
  5. In the Choose Filter list, select ClinVar.
    1. Select the top checkbox to select all values.
    2. Click Set.
  6. In the Choose Filter list, select Minor Allele Frequency.
    1. Enter a range value, then select Include boundary values.
    2. Click Set.
  7. In the Choose Filter list, select Variant Effect.
    1. Select the top checkbox to select all values.
    2. Click Set.
  8. Click Save.

Your filter chain can now be added to an analysis workflow, or applied to analysis results or a visualization. For more information, see Add a filter chain to an analysis workflow, Apply a filter chain to analysis results, and Use filter chains to change analysis results.

Example of a COSMIC, ClinVar, MAF, and Variant Effect filter chains applied to analysis results.

Related Topics
Parent topic: Custom filter chain examples