Filters

The Filters in the Analysis Tools tab help you narrow down millions of variants to just those most relevant for your case. You can adjust them manually or use preset combinations. Filters cover everything from variant quality and population frequency to inheritance models, phenotypic match, prediction scores, and user actions — giving you precise control over your review process.

Variants can be filtered by:

• 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.

  • In Simple Mode, the My Tags filter now applies to all tags you assigned to a variant.

  • In Advanced Mode, a new User Tags filter is available. This lets you filter by tags assigned by any user, not just yourself.

  • You can also filter for variants tagged by the AI shortlist or flagged at the organization level.

Filter modes

Filters can be applied in two ways:

• Simple Mode – Quick, high-level filtering (e.g., quality, severity, zygosity).

• Advanced Mode – Fine-grained filtering with expanded options, including user tags, prediction scores, and population thresholds.

Note: Quality, polymorphism and variant filters can operate in either a simple or advanced mode.

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Filter options menu

In the Filters tab of the Filters/Presets panel, the vertical ellipsis button offers these actions:

• Clear – Deselect all filters and reveal all variants.

• Reset to Default – Return to default filter settings:

  • Quality: Moderate/High

  • Variant severity: Low/Moderate/High

  • Proband zygosity: Het/Hom

• Save as Preset – Create a new preset based on your current active filters.

Tips:

• Use Simple Mode for quick case reviews and Advanced Mode for detailed interpretation workflows.

• The new User Tags filter is especially useful in collaborative environments where multiple reviewers tag variants differently.

Warning:

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