Manual filtering
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      2. AION - Instructions for Use
      3. Manual filtering

      Manual Filtering - small variants

      Additionally to the AION results tab, all annotated variants are available for analysis on Manual variant filtering - Small variant view.

      ⚠️ AION annotates all variants of the VCF file that are in the supported regions and has VCF FILTER value PASS or “.”

      Be aware that depending on your secondary analysis configuration this might mean also variants of low quality can be visualised and available for analysis through the manual filtering view! You can set filters for variant quality directly in the column filters, or utilising advanced filters.

      How it relates to the AION results tab

      The goal of AION is to provide high quality automated analysis so that users don’t have to use manual filtering of variants. The AION results tab is the best place to find relevant variants fast. It shortlists the variants that are relevant from a molecular and a clinical perspective, drastically improving the interpretation efficacy. For more details on the AION results (Smoking guns and AION Clues) visit the AION results page.

      However, in those cases where additional information is needed or it is simply desirable to double check whether no other relevant variants were present in a given region, it is possible to use the manual filtering. This could happen, for instance, when the case phenotype is not detailed enough to drive accurate clinical prioritization or when there is strong suspicion that the causative variant may be in regions not supported by the automatic pipeline (see details here).

      How to use it

      The manual filtering - small variants tab consists of:

      1. A filterable table with all annotated variants allowing one by one filtering in the column filters and sorting of results

      2. A advanced filters filter functionality ( see page for creating, editing and applying advanced cascading filter logic with just a few clicks , see more details Advanced filters

      Some variants may be listed multiple times if their position is a region of overlap between two genes. In that situation, the variant would be shown twice, one for each associated disease.

      Each variant in the table has a detailed view informing the user about its clinical relevance, linking it to one or more diseases (when available) as well as allowing the user to add the specific variant-disease pair to the report.