Pedersen Brent S, Quinlan Aaron R
Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, United States.
Bioinformatics. 2025 Mar 4;41(3). doi: 10.1093/bioinformatics/btaf097.
Variant call format (VCF) files are the standard output format for various software tools that identify genetic variation from DNA sequencing experiments. Downstream analyses require the ability to query, filter, and modify them simply and efficiently. Several tools are available to perform these operations from the command line, including BCFTools, vembrane, slivar, and others.
Here, we introduce vcfexpress, a new, high-performance toolset for the analysis of VCF files, written in the Rust programming language. It is nearly as fast as BCFTools, but adds functionality to execute user expressions in the lua programming language for precise filtering and reporting of variants from a VCF or BCF file. We demonstrate performance and flexibility by comparing vcfexpress to other tools using the vembrane benchmark.
vcfexpress is available under the MIT license at https://github.com/brentp/vcfexpress with code used for the manuscript deposited in https://doi.org/10.5281/zenodo.14756838.
变异调用格式（VCF）文件是各种从DNA测序实验中识别基因变异的软件工具的标准输出格式。下游分析需要能够简单高效地查询、过滤和修改这些文件。有几种工具可从命令行执行这些操作，包括BCFTools、vembrane、slivar等。
在此，我们介绍vcfexpress，这是一个用于分析VCF文件的全新高性能工具集，用Rust编程语言编写。它的速度几乎与BCFTools一样快，但增加了用Lua编程语言执行用户表达式的功能，以便从VCF或BCF文件中精确过滤和报告变异。我们通过使用vembrane基准测试将vcfexpress与其他工具进行比较，展示了它的性能和灵活性。
vcfexpress根据MIT许可协议可在https://github.com/brentp/vcfexpress获取，用于撰写本文的代码存于https://doi.org/10.5281/zenodo.14756838。
