Versions tab

The Versions tab provides a snapshot of all tools, data sources, and knowledge bases used during the analysis of a case. This feature supports traceability and reproducibility by documenting the exact versions of each resource involved in variant interpretation.

Reported categories

Annotation tools

This section lists automated tools used for variant-level annotation. Using computational models and predictive algorithms, they generate scores or classifications that help assess the potential impact of each variant.

Emedgene resources

This section includes Emedgene proprietary models and components that support variant prioritization and interpretation:

• ACMG tags algorithm

• AI Shortlist model "Tier v0" indicates focused mode, and "Tier v2" indicates discovery mode of the AI Shortlist model for rare diseases.

• Emedgene knowledge base

• Emedgene pipeline—tertiary analysis pipeline

• Emedgenizer plugin (v100.39.0+)

An Emedgenizer is a logic-based tool designed to normalize quality parameters in the VCF output from a specific variant caller, ensuring alignment with Emedgene internal format. An Emedgenizer is specific to the variant caller, its version, and the calling methodology used.

All Emedgenizers are grouped and versioned within an Emedgenizer Plugin.

Typically, the Emedgenizer Plugin version used for a case aligns with the pipeline version that processed it. However, updates to existing normalization logic, bug fixes, or the addition of support for new callers or methodologies may require updating or creating new Emedgenizers, which in turn necessitates a new plugin version. These changes are generally reflected in a minor version update of the Emedgenizer Plugin.

Documenting the version number is crucial for maintaining traceability in variant quality assessment.

• Phenocompare model

Input data

This section documents the input files used in the tertiary analysis pipeline. These include:

• Quality BED file—Defines regions used to evaluate sample quality

• Region of interest BED file—Specifies genomic intervals included in tertiary analysis

• Sample VCF files—Contain the variant calls generated during upstream analysis; associated individual Emedgenizer versions are also recorded

Knowledge base sources

This section documents the curated databases used to provide gene-level and disease-related information.

Organization local databases

This section includes organization-specific datasets integrated into the analysis.

Population databases

This section documents the variant frequency databases used to assess variant rarity and support pathogenicity classification.

Reference data

This section documents the reference genome assembly name and reference genome GenBank assembly accession number.

Variant databases

This section includes databases that support classification by providing information on previously observed variants.

Note: These versions remain static from the time a case is run. They are not updated unless a case is reanalyzed.

Current limitation: Reports generated within the system do not dynamically reflect the versions of the tools, data sources, and knowledge bases used.