Vcfexpress: flexible, rapid user-expressions to filter and format VCFs.
Brent S Pedersen1, Aaron R Quinlan1
1Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, United States.
Bioinformatics (Oxford, England)
|March 4, 2025
Summary
vcfexpress is a new, high-performance toolset for analyzing genetic variation in Variant Call Format (VCF) files. It offers efficient filtering and reporting using Lua scripting, rivaling existing tools like BCFTools.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Variant Call Format (VCF) files are standard for genetic variation data.
- Efficient querying, filtering, and modification of VCF files are crucial for downstream analyses.
- Existing command-line tools like BCFTools and vembrane offer some VCF manipulation capabilities.
Purpose of the Study:
- Introduce vcfexpress, a novel, high-performance toolset for VCF file analysis.
- Enhance VCF analysis with precise filtering and reporting using user-defined Lua expressions.
- Provide a flexible and efficient alternative to existing VCF analysis tools.
Main Methods:
- Developed vcfexpress using the Rust programming language for high performance.
- Implemented functionality to execute user expressions in the Lua programming language.
- Benchmarked vcfexpress against other VCF analysis tools, including BCFTools and vembrane.
Main Results:
- vcfexpress demonstrates high performance, comparable to BCFTools.
- The tool enables precise variant filtering and reporting through Lua scripting.
- Comparative benchmarks highlight vcfexpress's flexibility and efficiency.
Conclusions:
- vcfexpress offers a powerful and efficient solution for VCF file analysis.
- Its combination of speed and Lua scripting flexibility makes it a valuable tool for genomic data processing.
- The tool is readily available for use in various bioinformatics workflows.
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