Install freebayes with Homebrew, apt, Nix

Project links

• Homepage
• Upstream docs
• Package manager page

Commands and aliases

• bamleftalign
• freebayes

Project history

The GitHub repository was created in October 2010 and the license identifies Erik Garrison and Gabor Marth as 2010 copyright holders. The README cites the 2012 arXiv preprint 'Haplotype-based variant detection from short-read sequencing' and asks users to cite it when freebayes contributes to a publication.

freebayes was designed around literal read haplotypes rather than only precise alignment columns, generalizing earlier alignment-based variant detectors such as PolyBayes, samtools, and GATK. The README says the preprint was never submitted for review but has been used in over 1000 publications.

Release history shows a long-lived scientific command-line tool: v1.0.1 in 2015 helped downstream package management, v1.1.0 in 2016 integrated SeqLib for speed and memory improvements, v1.2.0 in 2018 changed default filters for sensitivity, v1.3.0 in 2019 added high-coverage skipping, and later 1.3.x releases focused on CRAM, Meson/Ninja, ARM64, Python 3, static builds, Debian/Ubuntu packaging, and dependency cleanup.

Adoption history

The README links badges or documentation for Bioconda, Homebrew, Guix, Debian, and other packaging contexts, and notes that GitHub release tarballs are used by Linux distributions to build and release freebayes binaries. The input package metadata also shows Homebrew, Debian, and Nix package coverage.

Adoption is also scientific rather than only packaging-based: the README's citation note says freebayes has been used in over 1000 publications, and its workflow examples place it among common genomics command-line tools such as bwa, sambamba, vcflib, bcftools, GATK, Picard, and workflow managers such as Snakemake.

How it is used

In simplest use, freebayes takes a FASTA reference and a sorted BAM or CRAM alignment file and emits VCF: freebayes -f ref.fa aln.bam > var.vcf. It also supports joint calling across multiple BAMs, GVCF output, high-coverage skipping, ploidy settings, pooled samples, forced calls from VCF alleles, and long-haplotype calling.

The README describes Unix-style pipeline use, including streaming BAM input from standard input, post-call filtering through vcflib's vcffilter, parallel execution by splitting the genome into regions, and Snakemake examples for cluster-friendly parallelism.

Why package nerds care

freebayes is package-nerd significant because it is a research-grade bioinformatics tool that distributions have had to keep buildable across changing C++ dependencies, Python versions, CRAM libraries, vcflib headers, and architecture targets. Its release notes read like a history of genomics packaging pain: vendored libraries, Meson migration, Debian build constraints, static binaries, Guix shells, and Bioconda-style tarballs.

It also embodies the classic Unix bioinformatics package model: a single-purpose CLI that reads standard genomics formats, writes VCF, composes with other tools, and can be sharded by genomic region for parallel execution.

Timeline

• 2010: GitHub repository created and MIT license copyright year recorded.
• 2012: Haplotype-based variant detection preprint published on arXiv.
• 2015: v1.0.1 released as a downstream-package-management-friendly bugfix release.
• 2016: v1.1.0 integrated SeqLib for speed and memory efficiency.
• 2018: v1.2.0 changed default filters for sensitivity.
• 2019: v1.3.0 added --skip-coverage for high-depth regions.
• 2020: v1.3.3 added CRAM support notes, Meson/Ninja builds, ARM64 compilation, Python 3 script updates, and GitHub CI.
• 2022: v1.3.6 added Snakemake parallel examples, Guix shell support, static builds, and performance tracking.
• 2024: v1.3.8 focused on Debian fixes and unbundling vcflib.
• 2025: v1.3.10 released with vcflib-path and build maintenance.

Related projects

• Related projects named in the official documentation include PolyBayes, samtools, GATK, vcflib, GNU parallel, Snakemake, bwa, sambamba, bcftools, Picard, htslib, SeqLib, Guix, Bioconda, Debian packaging, and CRAM/VCF/BAM ecosystem tools.

Sources

• https://api.github.com/repos/freebayes/freebayes
• https://arxiv.org/abs/1207.3907
• https://github.com/freebayes/freebayes
• https://github.com/freebayes/freebayes/blob/master/RELEASE-NOTES.md
• https://github.com/freebayes/freebayes/releases