Vcfexpress: flexible, rapid user-expressions to filter and format VCFs

Abstract

MotivationVariant 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. ResultsHere, 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. Availabilityvcfexpress is available under the MIT license at https://github.com/brentp/vcfexpress Contactbpederse@gmail.com, aquinlan@genetics.utah.edu Supplementary informationSupplementary data are available at Bioinformatics online.