Algorithmic filters

Algorithmic filters are very powerful filters allowing you to perform more complex variant filtering. These filters can be fully customized by our experts according to specific needs of your workflow. Use cases for algorithmic filters are almost infinite.

As an example, a custom made algorithmic filter is developed to:

  1. Keep any variants that fall either within or -50/+20 from the edges (except for the first and last exon) of coding exons of genes in a gene list, but only if they are within the transcript: exclude variants that are 50nt upstream of the first exon or 10 nt downstream of the last.
  2. Exclude variants that have variant fraction lower than 0.15.
  3. Exclude variants if they fall in positions with a coverage of less than 20.
  4. Keep only variants which match any of these conditions:
    • marked as Pathogenic or Likely Pathogenic by VarSome's ACMG classifier OR
    • marked as "Not provided" or "Uncertain Significance" or "Likely Pathogenic" or "Pathogenic" or "Drug Response" or "Drug Association" or "Risk Factor" or "Conflicting" or "Cancer" or "NA" or "Other" in ClinVar

Below you may find some algorithmic filters that are available on VarSome Clinical:

  • Recessive candidates
  • ACMG Actionable Gene
  • Carrier risk for couples
  • Compound Heterozygous + homozygous
  • Compound Heterozygous Candidates
  • Compound Heterozygous Segregating Variants
  • De novo (strict)
  • De novo candidates (naive)
  • Segregating Variants (dominant)
  • Segregating Variants (recessive)
  • Variants common to all affected samples

You can access Algorithmic filters under Launch analysis > Algorithmic filter analysis:

Menu

Once on the page with the list of all Algorithmic filters, you can always click on the blue circle to learn about details of each Algorithmic filter:

Details of Algorithmic filter

In other words, Algorithmic filters create a snapshot of the parent analysis, with a filtered subset of variants, according to each Algorithmic filter. Later on, you lay over Dynamic filters to fine-tune the list of your variants.

You can also find demonstrated examples of how to apply them in your analyses.

Algorithmic Filters offer a great deal of flexibility and can be fully adjusted according to your needs and your specific workflow. We can encode practically any kind of filtering criteria.

Please note that depending on the complexity of the desired filter the setup process may be subject to a fee.

Exonic & Splicing algorithmic filter

A special case of algorithmic filter is “Exonic and splicing” which only keeps exonic (including UTR and other non-coding exons) and splicing (no more than 10 nucleotides from a known splice site) variants. 

The filter may be launched manually, just like any other, but it will also be run automatically on any analyses with more than 500 000 variants. 

This algorithmic filter provides the same results as would occur if you made a dynamic filter with the following criteria:

  • Coding
  • Splicing
  • Non-coding exon +3’ utr
  • Non-coding exon +5’ utr 

The aim of this filter, and the reason it will run automatically for large analyses, is to provide a smaller subset of results to the user which will be far quicker and easier to sort through. Since, even with WGS analyses, the variants of interest tend to be those that can affect the protein sequence, we feel that this filter will help our users quickly identify and focus on the variants of interest even on larger samples such as WGS.

 

Please note that while the filter will be run automatically for such large analyses, the full result set will still be available as usual. The filter will run as a sub-analysis and will not affect the results of the main, parent analysis in any way.