CITATION.cff

cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: "Vcfexpress: flexible, rapid user-expressions to filter and format VCFs"
abstract: "Motivation 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. Results 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."
authors:
  - family-names: Pedersen
    given-names: Brent S.
    email: bpederse@gmail.com
  - family-names: Quinlan
    given-names: Aaron R.
    email: aquinlan@genetics.utah.edu
type: software
doi: 10.1101/2024.11.05.622129
year: 2024
journal: bioRxiv
repository-code: https://github.com/brentp/vcfexpress
license: MIT
identifiers:
  - type: doi
    value: 10.1101/2024.11.05.622129
    description: The bioRxiv preprint
references:
  - type: article
    authors:
      - family-names: Pedersen
        given-names: Brent S.
      - family-names: Quinlan
        given-names: Aaron R.
    title: "Vcfexpress: flexible, rapid user-expressions to filter and format VCFs"
    year: 2024
    journal: bioRxiv
    doi: 10.1101/2024.11.05.622129