BCFtools Unofficial Windows Bundle

This repository publishes a small Windows x64 bundle of bcftools.exe copied from the MSYS2 UCRT64 environment, together with the runtime DLLs needed to run it from a single directory.

This is an unofficial Windows bundle. It is not published, endorsed, or supported by the official BCFtools/HTSlib project.

Official BCFtools site: https://www.htslib.org/

Included Version

• BCFtools: 1.23.1
• HTSlib: 1.23.1
• Source environment: MSYS2 UCRT64
• Target platform: Windows x64

Usage

Download the release ZIP from:

https://github.com/win-ngs/bcftools-windows-bundle/releases/tag/v1.23.1-windows-ucrt64

Extract it, and run:

.\bcftools.exe --version

The executable and DLLs are intended to stay in the same directory.

BCFtools plugins are included in the plugins directory. To use bcftools +plugin commands from PowerShell, set the plugin path first:

$env:BCFTOOLS_PLUGINS = "$PWD\plugins"
.\bcftools.exe plugin -l

You can add the extracted directory to PATH if you want to run bcftools from any shell.

License

BCFtools is distributed under the MIT/Expat license. See LICENSE.md.

This bundle also includes third-party DLLs from MSYS2 packages. See THIRD_PARTY_NOTICES.md and the licenses/ directory in the release archive.