Install vcftools with Homebrew, apt, dnf, MacPorts, Nix

Project links

• Homepage
• Repository
• Upstream docs
• Package manager page

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

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

• https://api.github.com/repos/vcftools/vcftools/releases
• https://pubmed.ncbi.nlm.nih.gov/21653522/
• https://vcftools.github.io/
• https://vcftools.github.io/links.html
• https://vcftools.sourceforge.net/