Filters

Use the Filters tab in the Filters/Presets panel to narrow numerous variants down to those most relevant to your case.

Filter categories

Filter group	Purpose	Different modes
Quality filters	Narrow variants by sequencing quality metrics such as depth, mapping quality, and confidence grade
Polymorphism filters	Filter by allele frequency and genotype counts from public databases (e.g., gnomAD, ExAC) or your lab’s internal controls
Variant type filters	Focus on specific variant categories (SNVs, indels, CNVs, SVs, STRs, mtDNA)
Variant effect filters	Select by predicted consequences on genes or proteins, ACMG classes, or database classifications
In silico prediction filters	Apply computational prediction scores for pathogenicity, conservation, splicing, or missense effects
Gene filters	Restrict results to genes of interest, such as disease–associated, candidate, ACMG actionable, or cancer–related genes
Phenomatch filters	Highlight variants in genes with known disease associations matching the proband’s phenotypes
Inheritance filters	Filter variants according to inheritance patterns consistent with family genotypes and phenotypes
Zygosity filters	Select by genotype status (Het, Hom, Hemi) in specific samples
Evidence & Tags filters	Show variants tagged by users, AI shortlist, or flagged at the organization level

Applying multiple filters at once may exclude important variants if thresholds are too strict. Start broad, then refine.

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.

Simple and advanced filtering modes operate independently.

Even with similar settings, results may differ 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.

Filters actions menu

When the Filters tab of the Filters/Presets panel is selected, click the vertical ellipsis in the top-left corner to access the following actions:

• Clear: Clears all filters and displays all variants in the case

• Reset to default: Clears all filters and applies default settings

• Save as preset: Saves the current filter configuration as a new preset

Default filtering settings

When filters are reset to default, Emedgene applies a few essential baseline filters for a broad and reliable starting point for variant review. The table below lists the only filters automatically activated by default. All other filters remain inactive and impose no restrictions on the results unless the user turns them on manually.

Filter group	Filter	Setting
Quality filters	Quality	Moderate, High
Quality filters	Mapping Quality	≥45
Quality filters	Depth	≥10
Variant effect filters	Severity	Low, Moderate, High
Zygosity filters	Proband zygosity	Het, Hom
Gene filters	Candidate genes	Active (only in cases analyzed with a gene list)