macOS
Homebrewverified · 100%
brew install vcftoolslocal Homebrew formula metadata
MacPortsverified · 94%
sudo port install vcftoolsMacPorts ports tree · science/vcftools/Portfile · source: api.github.com
brew / rank 5477
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. Also installable with debian: sudo apt install vcftools.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install vcftoolsDebian stable package indexes · vcftools · source: deb.debian.org
Fedora dnfverified · 92%
sudo dnf install vcftoolsFedora Rawhide package metadata · vcftools · source: dl.fedoraproject.org
Nixverified · 92%
nix profile install nixpkgs#vcftoolsnixpkgs package indexes · pkgs/by-name/vc/vcftools/package.nix · source: api.github.com
overview
Package summary
Tools for working with VCF files
Project links
Commands and aliases
- fill-aa
- fill-an-ac
- fill-fs
- fill-ref-md5
- vcf-annotate
- vcf-compare
- vcf-concat
- vcf-consensus
- vcf-contrast
- vcf-convert
- vcf-fix-newlines
- vcf-fix-ploidy
- vcf-indel-stats
- vcf-isec
- vcf-merge
- vcf-phased-join
- vcf-query
- vcf-shuffle-cols
- vcf-sort
- vcf-stats
- vcf-subset
- vcf-to-tab
- vcf-tstv
- vcf-validator
- vcftools
history
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 posture
Risk level: green
narrow executable package without higher-risk signals.
Risk classifier
green risk · low confidence · appliance
Why
- narrow executable package without higher-risk signals
Signals
- metadata:no-higher-risk-signals
Install behavior
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
fill-aa | executable | indexed executable | Discovered from the local executable index. |
fill-an-ac | executable | indexed executable | Discovered from the local executable index. |
fill-fs | executable | indexed executable | Discovered from the local executable index. |
fill-ref-md5 | executable | indexed executable | Discovered from the local executable index. |
vcf-annotate | executable | indexed executable | Discovered from the local executable index. |
vcf-compare | executable | indexed executable | Discovered from the local executable index. |
vcf-concat | executable | indexed executable | Discovered from the local executable index. |
vcf-consensus | executable | indexed executable | Discovered from the local executable index. |
vcf-contrast | executable | indexed executable | Discovered from the local executable index. |
vcf-convert | executable | indexed executable | Discovered from the local executable index. |
vcf-fix-newlines | executable | indexed executable | Discovered from the local executable index. |
vcf-fix-ploidy | executable | indexed executable | Discovered from the local executable index. |
vcf-indel-stats | executable | indexed executable | Discovered from the local executable index. |
vcf-isec | executable | indexed executable | Discovered from the local executable index. |
vcf-merge | executable | indexed executable | Discovered from the local executable index. |
vcf-phased-join | executable | indexed executable | Discovered from the local executable index. |
vcf-query | executable | indexed executable | Discovered from the local executable index. |
vcf-shuffle-cols | executable | indexed executable | Discovered from the local executable index. |
vcf-sort | executable | indexed executable | Discovered from the local executable index. |
vcf-stats | executable | indexed executable | Discovered from the local executable index. |
vcf-subset | executable | indexed executable | Discovered from the local executable index. |
vcf-to-tab | executable | indexed executable | Discovered from the local executable index. |
vcf-tstv | executable | indexed executable | Discovered from the local executable index. |
vcf-validator | executable | indexed executable | Discovered from the local executable index. |
vcftools | executable | indexed executable | Discovered from the local executable index. |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-08-03
manager version0.1.17
manager updated
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:vcftools |
|---|---|
| Version | 0.1.17 |
| Package manager | Homebrew |
| Homepage | https://vcftools.github.io/ |
| Repository | https://github.com/vcftools/vcftools |
| Bottle | not recorded |
| Service | none declared |
source database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
Debian apt95%
vcftools 0.1.16-3+b1
Collection of tools to work with VCF files
sudo apt install vcftools- Section: science
- Architecture: amd64
- Source Package: vcftools
- 5 dependencies
- 1 optional deps
- normalized package name match
- Matched by: Vcftools
Nix95%
vcftools
nix profile install nixpkgs#vcftools- normalized package name match
- Matched by: Vcftools
Ubuntu apt95%
vcftools 0.1.16-3
Collection of tools to work with VCF files
sudo apt install vcftools- Section: universe/science
- Architecture: amd64
- 5 dependencies
- 1 optional deps
- normalized package name match
- Matched by: Vcftools
dnf95%
vcftools 0.1.17-3.fc45
VCF file manipulation tools
sudo dnf install vcftools- License: GPL-3.0-only
- Category: Unspecified
- Architecture: x86_64
- Source Package: vcftools
- 9 dependencies
- 2 provides
- normalized package name match
- Matched by: Vcftools
MacPorts95%
vcftools
sudo port install vcftools- normalized package name match
- Matched by: Vcftools
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- pkg.so package database
- pkgdb category and tag curation