VCFFilterJS

VCFFilterJS filters Variant Call Format (VCF) files using JavaScript to apply programmable variant-filtering criteria within genomic data processing workflows.

Key Features:

• JavaScript-Based Filtering: Utilizes JavaScript to define and evaluate complex filtering criteria on VCF records.
• Java Rhino Engine: Executes JavaScript within the Java Rhino engine to run filters in Java environments.
• Integration with Jvarkit: Distributed as part of the Jvarkit suite of bioinformatics tools.

Scientific Applications:

• Custom Variant Filtering: Applies bespoke filtering expressions to select or exclude variants based on record fields and annotations.
• Pipeline Integration: Embeds programmable filtering steps into Java-based genomic data processing pipelines.
• Method Development: Facilitates testing and application of novel filtering criteria in variant analysis workflows.

Methodology:

Executes user-provided JavaScript expressions on Variant Call Format (VCF) records using the Java Rhino engine.