# Install vcftools with Homebrew, apt, dnf, MacPorts, Nix Tools for working with VCF files. Version 0.1.17 via Homebrew; verified from local package data. ## Install ```sh sudo av install brew:vcftools ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install vcftools ``` Evidence: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install vcftools ``` Evidence: MacPorts ports tree: science/vcftools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ### Linux - Debian apt (92%): ```sh sudo apt install vcftools ``` Evidence: Debian stable package indexes: vcftools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - dnf (92%): ```sh sudo dnf install vcftools ``` Evidence: Fedora Rawhide package metadata: vcftools from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst - Nix (92%): ```sh nix profile install nixpkgs#vcftools ``` Evidence: nixpkgs package indexes: pkgs/by-name/vc/vcftools/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## Package facts - **Package key:** brew:vcftools - **Package manager:** Homebrew - **Package manager page:** - **Version:** 0.1.17 - **Source summary:** Tools for working with VCF files - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** LGPL-3.0-only - **Source archive:** - **Generated:** 2026-07-08T18:08:21+00:00 ## Executables - fill-aa (cli) - fill-an-ac (cli) - fill-fs (cli) - fill-ref-md5 (cli) - vcf-annotate (cli) - vcf-compare (cli) - vcf-concat (cli) - vcf-consensus (cli) - vcf-contrast (cli) - vcf-convert (cli) - vcf-fix-newlines (cli) - vcf-fix-ploidy (cli) - vcf-indel-stats (cli) - vcf-isec (cli) - vcf-merge (cli) - vcf-phased-join (cli) - vcf-query (cli) - vcf-shuffle-cols (cli) - vcf-sort (cli) - vcf-stats (cli) - vcf-subset (cli) - vcf-to-tab (cli) - vcf-tstv (cli) - vcf-validator (cli) - vcftools (cli) - fill-aa (alias) - fill-an-ac (alias) - fill-fs (alias) - fill-ref-md5 (alias) - vcf-annotate (alias) - vcf-compare (alias) - vcf-concat (alias) - vcf-consensus (alias) - vcf-contrast (alias) - vcf-convert (alias) - vcf-fix-newlines (alias) - vcf-fix-ploidy (alias) - vcf-indel-stats (alias) - vcf-isec (alias) - vcf-merge (alias) - vcf-phased-join (alias) - vcf-query (alias) - vcf-shuffle-cols (alias) - vcf-sort (alias) - vcf-stats (alias) - vcf-subset (alias) - vcf-to-tab (alias) - vcf-tstv (alias) - vcf-validator (alias) - vcftools (alias) ## Dependencies - htslib ## Build dependencies - pkgconf ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 0.1.17 - Local data: ok - Upstream repository: https://github.com/vcftools/vcftools - info: No package-manager update timestamp was available. - info: No cached GitHub release or tag data was available. ## Project history and usage VCFtools is the classic command-line suite and Perl API for working with Variant Call Format files. Its history is inseparable from the standardization of VCF itself: the 2011 Bioinformatics paper introduced the format and the toolkit together in the context of the 1000 Genomes Project. ### Project history Danecek and collaborators published "The variant call format and VCFtools" in Bioinformatics in 2011. The paper describes VCF as a format for SNPs, insertions, deletions, structural variants, rich annotations, compression, and indexed retrieval, and states that it was developed for the 1000 Genomes Project. The original VCFtools site describes the project as a package for VCF files such as those generated by the 1000 Genomes Project. It consists of a Perl module for manipulating VCF files and a binary executable for general analysis routines. ### Adoption history The 2011 paper records early adoption beyond 1000 Genomes, including UK10K, dbSNP, and the NHLBI Exome Project. That early institutional adoption made VCFtools one of the first practical command-line entry points for a format that later became routine in sequencing workflows. The SourceForge-era project moved to GitHub in July 2015, according to the old project homepage. GitHub releases show an initial GitHub release in August 2015, later v0.1.14, v0.1.15, v0.1.16, and a v0.1.17 release in May 2025, showing long-tail maintenance of a mature tool. ### How it is used VCFtools is used to filter variants, compare VCF files, summarize variant sets, convert formats, validate files, merge records, and create intersections or subsets. Its command set includes both the main `vcftools` binary and legacy Perl utilities such as `vcf-annotate`, `vcf-merge`, `vcf-query`, and `vcf-validator`. In practice, it is often used for cohort-level filtering and summary statistics: missingness thresholds, allele-frequency filters, site and genotype quality filters, sample subsets, recoding, and quick sanity checks before or after more specialized tools. ### Why package nerds care VCFtools is package-nerd significant because it is one of the canonical packages that made VCF a usable Unix file format, not just a paper specification. It gave users validators, filters, mergers, converters, and a Perl API at the moment large sequencing projects needed reproducible file handling. Even when newer tools such as bcftools, vcflib, cyvcf2, and specialized annotators are preferred for particular tasks, VCFtools remains a recognizable baseline package in bioinformatics environments and container images. ### Timeline - 2011-06-07: The VCFtools paper appears online ahead of print. - 2011-08-01: The VCFtools paper is published in Bioinformatics volume 27, issue 15. - 2015-07: The VCFtools project moves from SourceForge to GitHub. - 2015-08-03: v0.1.13 is published as the initial GitHub release. - 2025-05-15: v0.1.17 is published on GitHub. ### Related projects - The 1000 Genomes Project is the original project context for VCF and VCFtools. - HTSlib and bcftools are closely related tools for modern VCF/BCF processing. - vcflib, VcfPythonUtils, and vcfCTools are listed by VCFtools as useful related VCF projects. - GATK is listed by VCFtools as another source and manipulator of VCF files. ### Sources - - - - - ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** vcftools - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Other Package-Manager Records - Debian apt - vcftools - 0.1.16-3+b1: normalized package name match | Debian stable package indexes: vcftools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Collection of tools to work with VCF files | https://vcftools.github.io/ - Nix - vcftools: normalized package name match | nixpkgs package indexes: pkgs/by-name/vc/vcftools/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - vcftools - 0.1.16-3: normalized package name match | Ubuntu 24.04 LTS package indexes: vcftools from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Collection of tools to work with VCF files | https://vcftools.github.io/ - dnf - vcftools - 0.1.17-2.fc44: normalized package name match | Fedora Rawhide package metadata: vcftools from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst | VCF file manipulation tools | https://vcftools.github.io/ - MacPorts - vcftools: normalized package name match | MacPorts ports tree: science/vcftools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ## Related links - [Source-control packages](https://www.automicvault.com/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [htslib](https://www.automicvault.com/pkg/brew/htslib/) - Runtime dependency declared by Homebrew. - [pkgconf](https://www.automicvault.com/pkg/brew/pkgconf/) - Build dependency declared by Homebrew. - [vcflib](https://www.automicvault.com/pkg/brew/vcflib/) - Shares av.db curated category or tags: bioinformatics, c-plus-plus, cli, genomics, science. - [vcfanno](https://www.automicvault.com/pkg/brew/vcfanno/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, vcf. - [abricate](https://www.automicvault.com/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [gffread](https://www.automicvault.com/pkg/brew/gffread/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [minigraph](https://www.automicvault.com/pkg/brew/minigraph/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [stringtie](https://www.automicvault.com/pkg/brew/stringtie/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [tabixpp](https://www.automicvault.com/pkg/brew/tabixpp/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [bioperl](https://www.automicvault.com/pkg/brew/bioperl/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, perl, science. - [freebayes](https://www.automicvault.com/pkg/brew/freebayes/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, genomics, htslib, science. ## Combined YAML source View the package source record on GitHub. [combined/vcftools.yml](https://github.com/automic-vault/db/blob/main/combined/vcftools.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph