Simple filter operators mode
Simple filter operators mode
Simple filter operators mode is designed to filter variants using the system’s predefined logic. The logic that combines filters is predefined and is not shown or configurable in the UI.
Use Simple filter operators mode for common filtering scenarios where explicit control over filtering logic is not required. If you need to control how conditions are combined or access additional filters, switch to Advanced filter operators mode.
Tip: Applying multiple filters at once may exclude important variants if thresholds are too strict. Start broad, then refine.
Filter categories
Filters are organized by category. Each category contains filters that apply to a specific aspect of variant interpretation.
Narrow variants by sequencing quality metrics such as depth, mapping quality, and confidence grade
Filter by allele frequency and genotype counts from public databases (e.g., gnomAD, ExAC) or your lab’s internal controls
Focus on specific variant categories (SNVs, indels, CNVs, SVs, STRs, mtDNA)
Select by predicted consequences on genes or proteins, ACMG classes, or database classifications
Apply computational prediction scores for pathogenicity, conservation, splicing, or missense effects
Restrict results to genes of interest, such as disease–associated, candidate, ACMG actionable, or cancer–related genes
Highlight variants in genes with known disease associations matching the proband’s phenotypes
Filter variants according to inheritance patterns consistent with family genotypes and phenotypes
Select by genotype status (Het, Hom, Hemi) in specific samples
Show variants tagged by users, AI shortlist, or flagged at the organization level
Filtering modes
Quality, Polymorphism, Variant effect, In silico prediction, and Evidence & Tags filters can operate in either a simple or advanced mode.
Use simple mode for quick, high-level filtering. For more detailed filtering with expanded options, choose advanced mode to gain deeper control over filter parameters.
Filter settings are saved separately for each filtering mode per filter category for the current session. Switching between modes does not clear or merge those settings.
Simple and advanced filtering modes operate independently
Simple and advanced filtering modes operate independently.
Even with similar settings, results may differ between modes due to variations in filtering logic and options available.
For example, setting Severity to "High" in simple mode might yield slightly different results than selecting all high severity Main effect options in advanced mode of Variant effect filters.
Understand category-level filtering modes vs filter operators modes
Per-category filtering modes are available for some filter categories in Simple filter operators mode. They affect the options available within that category:
Simple: High-level filters.
Advanced: Expanded filters.
Filter operators modes define how filters are combined in the Filters tab:
Simple: Filtering logic is implicit.
Advanced: Filtering logic is explicit and user-defined.
Learn more about filter operators modes here.
Switch between filtering modes
In Analysis tools, open the Filters tab.
Enter the Simple filter operators mode and expand the filter category of interest.
Select Advanced on top of the filter group to enter Advanced filtering mode for this category.
To return to Simple filtering mode, select Simple.
Result: The selected filtering mode is enabled. If you previously configured filters in that mode, they remain available.
Actions menu
In the Filters tab, select vertical ellipsis () in the top-left corner to access the Actions menu.
Clear
Clears all filters and displays all variants in the case.
Reset to default
Clears all filters and applies default filtering conditions.
Note: The Reset to default action in the Filters tab behaves differently from the one in the Presets tab, where it clears only variant search refinements applied on top of the active preset group.
Save as preset
Saves the current filter configuration as a new preset to be reused across cases.
Default filtering settings
When filters are reset to default, Emedgene applies a few baseline filters for a broad starting point for variant review. The table below lists the filters automatically activated by default. All other filters remain inactive and impose no restrictions on the results unless the user turns them on manually.
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