Franklin offers advanced filtering tools to support accurate and streamlined compound heterozygous (compound het) variant analysis. One of the most powerful tools available for this purpose is the "Tree Compound" filter, designed specifically for SNVs and indels.
This article explains what the Tree Compound filter does, how it works, and how to use it effectively in your analysis workflows.
What is the Tree Compound Filter?
The Tree Compound filter outputs only paired variants within the same gene, designed to support compound het analysis. It ensures:
Both variants are retained only if they form a valid compound het pair. This allows the user to define previous filtration logic based on variant-level characteristics (e.g., consequence, classification)
In family contexts, inheritance is automatically considered meaning variants must be inherited from different parents or be de novo variants.
Two Ways to Use the Tree Compound Filter
The Tree Compound filter can be configured in two different ways, depending on whether one or two branches are connected upstream:
1. Single-Branch Configuration
If you connect only one branch to the Tree Compound filter:
The filter will return only variants that have at least one additional variant in the same gene, from the same input list.
In other words, it identifies genes with multiple qualifying variants, where both variants originate from the same filter path.
Use Case Example:
You have a list of filtered variants based on consequence and population frequency, and you want to find genes with two or more such variants, regardless of classification.
2. Dual-Branch Configuration
If you connect two branches to the Tree Compound filter:
The filter will only return variant pairs that come from different input branches, but belong to the same gene.
This enables cross-pairing between two distinct variant groups based on different criteria.
Use Case Example:
You want to identify compound het pairs where:
One variant is classified as Pathogenic (Branch A)
The other is a VUS (Branch B)
The filter will exclude any gene where both variants come from the same branch, ensuring clear logic separation and precise results.