Samtools Unofficial Windows Bundle

This repository publishes a small Windows x64 bundle of samtools.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 Samtools/HTSlib project.

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

Included Version

• Samtools: 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/samtools-windows-bundle/releases/tag/v1.23.1-windows-ucrt64

Extract it, and run:

.\samtools.exe --version

The executable and DLLs are intended to stay in the same directory. You can add the extracted directory to PATH if you want to run samtools from any shell.

License

Samtools 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.