You can refine a finished analysis by:
- Filtering by gene list
- Applying an algorithmic filter
- Detecting Copy Number Variants (CNVs)
Gene list analysis
Filter the results of a finished analysis to show only those variants falling within the genes given (including 500bp up and downstream flanking regions).
- Analysis: choose the analysis to be filtered.
- Gene List: choose a gene list to filter by. For more details see: Gene lists
- Phenotypes: choose a list of phenotypes. A gene list will be built using the genes associated with the chosen phenotypes. When building a gene list from phenotypes, you may choose to select genes associated with all of the provided phenotypes or genes associated with any of them.
The methodology to generate a gene list from phenotype(s) has been changed. Previously, when making a gene list from phenotypes, only those genes that are directly annotated with that phenotype were included. We have now extended this and instead first collect all diseases linked to the phenotype and then all genes linked to those diseases, as well as any genes directly linked to the phenotype. We already worked this way when adding phenotypes to analyses, so this change ensures we are consistent and also makes sure we don't miss any genes when creating gene lists.
You can apply sophisticated filters to perform more complex variant filtering to finished analyses.
You can access Algorithmic filters under Launch analysis > Algorithmic filter analysis as shown in the picture below.
To start an algorithmic filter, choose the target analysis, select an algorithmic filter, and then click on Start analysis.
For further details on the algorithmic filter and the provided parameters please click on the info icon next to the “Options” button.
As you can see for several of the existing filters we provide the option to change specific parameters. That way you can customize each of those filters according to your needs.
If you want to change a parameter click on the light blue “Options” button:
For example, if you want to change the default parameters for the filter "Max other samples (n≥1)", after you choose from the drop-down the analysis to which you wish to apply one or more filters, you then need to select the filter "Max other samples (n≥1)" by clicking the relevant check-box, which will in turn activate the Options box.
Now you can change the default value for this filter, by changing the number in the Maxim number of samples field and then by clicking on "Save".
Once the analysis has run, you can view the filter options selected for the algorithmic filter analysis both in the sub-analysis name
and in the “Sample analysis information” option of the “Analysis actions” menu:
For some of these filters, in order to add the parameterization functionality we have integrated similarly functioning filters into one. For example, you can now find under the filter “Segregating Variants”, the filters previously known as:
- Segregating Variants (dominant, all VUS),
- Segregating Variants (dominant, strong VUS)
- Segregating Variants (recessive, all VUS)
- Segregating Variants (recessive, strong VUS)
- Compound Heterozygous Segregating Variants (all VUS)
- Compound Heterozygous Segregating Variants (strong VUS).
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:
- 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.
Later on, you lay over Dynamic filters to fine-tune the list of your variants.
VarSome Picks is an advanced algorithmic filter, designed to empower bioinformatic analysis of genomic variants using AI. This tool goes beyond conventional variant prioritization methods by considering essential parameters such as phenotype, gene, and variant data, all within a disease-specific context. Its primary objective is to rank potentially causative variants, aiding researchers and clinicians in identifying significant genetic associations related to specific diseases.
You can find more information about VarSome Picks here.
Please, visit the article CNV/SV analysis to find out how to run a CNV analysis from FASTQ or VCF.
The subanalyses will be displayed as an additional tab next to the analysis title on the main page of analyses. You can easily switch between analyses by clicking on the respective tab.
For further details, please refer to the following link: https://docs.varsome.com/en/tabs