The Filter Decision Tree feature offers a visual and flexible way to build filtration logic, making it easier to refine your variant analysis. With the intuitive tree builder, you can create complex filtering conditions using "And/Or" logic and merge multiple nodes to define the exact criteria needed. This interactive canvas empowers you to design any logical structure, making the filtration process more transparent and dynamic.
Creating a New Filter Tree
To create a new filter tree, go to the assets page and click on the filter tree tile labeled "Create New". Provide a name for the filter tree, select the case type (single or family), choose the variant type (currently supporting only SNV/indel), and select the assays to which this tree will be applied. You can always add or modify the assays after the tree has been created.
Building Your Decision Tree
Use the canvas to create the filtration logic by dragging and dropping the relevant filters. Start by connecting the filter to the input variant circle, and continue adding filtration steps one by one. Each filter will add specific criteria, along with a "No Match" option, which will capture all variants that do not pass the previous filtration conditions.
To merge multiple nodes, add the "Merge Results" option and connect the lines from different nodes. This allows you to create "OR" logic, combining different filter results into a single path.
Editing a filter can be done by hovering over the filter, and clicking on the pencil icon. This will open a dialog that allows you to change the values.
Using the No Match branch can be useful to rescue variants that do pass other filtration criteria. For example, variants that are not classified as P/LP but are in splice regions and have high spliceAI prediction score:
Adding Quick Filter Labels
To add quick filter labels, hover over the desired result, and a label option will appear. Quick filter labels will be displayed in the Quick Filters section of the analysis, showing all variants that meet the filtering criteria up to that point. You can add multiple quick filter labels within a single decision tree, and all of them will be presented in the case.
Examples:
AND logic - Variant is Pathogenic or Likely pathogenic AND Exonic
OR logic - Variant is Pathogenic or Likely pathogenic OR Exonic
Saving Your Decision Tree
Once your decision tree is ready, click Save to add it to your assets. Please note that once a filter tree is saved, it cannot be edited. If you need to make changes, you will need to clone the tree to create a new version. Instructions for cloning are provided below.
Using Filter Trees in Analysis
After connecting a filter tree to the relevant assays, all newly annotated cases for that assay will automatically use the quick filters defined in the tree. Variants will be flagged with their relevant tags, and a variant can be flagged with multiple labels. To understand the filters used in a specific quick filter, open the Tree Viewer, which will also display the number of variants passing through each step.
Cloning a Filter Tree
To clone a filter tree, open the desired decision tree and select "Clone". This will prompt you to name the new version of the tree. After creating the new tree, you will need to manually disconnect the previous version from the respective assays. To do this, click on the context menu and select "Edit Tree Properties".