Apply Variant Filters
Last updated
Was this helpful?
Last updated
Was this helpful?
Variants filters provide options for applying any combination of inclusion and exclusion criteria to the variants in a case. Filter criteria can vary depending on the selected variant categories. If filters are applied to more than one variant category in the same filter group, only filters relevant for all variant categories are available. For more information, refer to .
Each filter combination resides on a different tab in the variant grid. Default filter views are defined in the test definition. You can create filter tabs in the grid for as many additional views as necessary. Filters applied in the variant grid are specific to the selected case.
For more information about filter options, refer to and
When you configure a new test, you can add one or more specific filters to the test definition. The filters become default filters and are applied to every case in your workgroup. The default filters are locked and shown in the first tabs of the variant grid. For more information, refer to .
The default filter tabs, indicated by a lock, cannot be altered or deleted for the cases already processed. To change or delete default filters, you must update the filters that are used in the test definition and reprocess the case and upcoming cases through the updated test definition.
Included with Connected Insights, a demonstration of the filtering is provided as a template for you to define your own filter views. In the primary filter group, the filter is set up to return all variants categories (ie small variants, copy number variants, structural variants, RNA fusion variants, and RNA splice variants) and requiring that these are called with a PASS by each of the variant callers. In the subsequent filter groups, the filter is set up to apply the following logic for each of the variant categories:
Small variants with coding consequences and population frequency ≤ 0.05 in gnomAD for AFR, AMR, EAS, NFE, SAS
Any copy number variants
Structural variants resulting in a unidirectional gene fusion with at least three supporting reads
RNA fusion variants resulting in a unidirectional gene fusion
RNA splice variants resulting in an exon loss
Configure and modify case-specific filter views in new or unlocked variant grid tabs. The default filter tabs, indicated by a lock, cannot be altered or deleted.
Create a tab using one of the following methods:
To create a filter, select New Filter.
To copy an existing filter, select the tab drop-down arrow and then select Duplicate Filter.
To load a new filter, select Load Filter.
Select or search for a filter to load from the list of compatible filters created and saved by all users in your workgroup. Filters with variant flags are only compatible to the cases using the same flag list. Select Apply.
[Optional] Double-click the tab label and enter a new name.
Select Edit Variant Filters.
Select Apply.
To lock a filter view, select the tab drop-down arrow, and then select Lock Filter. Locked filter views are indicated by a blue lock and cannot be deleted.
To edit a filter name, select the tab drop-down arrow, and then select Edit Filter Name.
After editing the name, select Save.
To save a filter view, select Edit Variant Filters, then select Save As. The filter is saved and can be configured in the test definitions to be a default filter and be used across cases. Column configurations and filter dependencies are saved with the filter.
To remove a filter view, delete the tab. Default tabs are indicated by a lock and cannot be deleted.
Export a list of variants and variant data to a tab-delimited file.
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.
Configure the filters and flags to show only the variants to export.
Select the tab drop-down arrow, and then select Export Grid as TSV.
Build and edit variant filters by applying various filtering criteria to the gene and variants. For more information, refer to .