brew / rank 10379

Install vcflib with Homebrew

C++ library and cmdline tools for parsing and manipulating VCF files. Version 1.0.15 via Homebrew; verified 2026-06-21.

Install command Security notes

install

Additional install commands

macOS

Homebrewverified · 100%

brew install vcflib

local Homebrew formula metadata

overview

Package summary

C++ library and cmdline tools for parsing and manipulating VCF files

Project links

Homepage

Commands and aliases

abba-baba
bFst
bed2region
bgziptabix
dumpContigsFromHeader
genotypeSummary
hapLrt
iHS
meltEHH
normalize-iHS
pFst
pVst
permuteGPAT++
permuteSmooth
plotHaps
popStats
segmentFst
segmentIhs
sequenceDiversity
smoother
vcf2bed.py
vcf2dag
vcf2fasta
vcf2sqlite.py
vcf2tsv
vcf_strip_extra_headers
vcfaddinfo
vcfafpath
vcfallelicprimitives
vcfaltcount
vcfannotate
vcfannotategenotypes

history

Project history and usage

vcflib is both a C++ library and a large collection of command-line utilities for parsing, transforming, filtering, normalizing, annotating, and summarizing VCF files. It is one of the Unix-style toolkits that grew around VCF after the format became the standard interchange format for genomic variant calls.

Project history

The vcflib README presents VCF as the de facto reporting format for many genomic variant detectors and describes vcflib as an API plus a command-line utility collection for complex VCF manipulation. The project originated with Erik Garrison and later became part of a broader vcflib organization containing related VCF tools.

In 2022, Garrison, Kronenberg, Dawson, Pedersen, and Prins published a PLOS Computational Biology software paper covering vcflib, bio-vcf, cyvcf2, hts-nim, and slivar. The paper describes more than 125 free and open-source tools and libraries for VCF processing, with vcflib providing performance-oriented C++ tools and a reusable API.

Adoption history

The 2022 PLOS paper states that VCF has been widely adopted since 2011 in population studies and somatic and germline mutation studies, and that the authors' tools run in critical biomedical pipelines and many shell scripts. That is the adoption setting in which vcflib matters: it is a toolbox for the messy middle of sequencing workflows.

The project has seen packaging and maintenance transitions common to mature bioinformatics software. GitHub releases show a 1.0 release in September 2019, a Python 3 transition around 2019, and continued 1.x releases into the 2020s.

How it is used

vcflib tools are designed to be composed in streaming pipelines. The README explicitly encourages using Unix pipes to interface with VCFtools, BEDTools, GATK, HTSlib, bio-vcf, bcftools, and FreeBayes while avoiding unnecessary intermediate files.

Typical commands cover filtering, set operations, left-aligning indels, decomposing or merging alleles, checking reference consistency, generating statistics, population-genetics metrics, converting VCF to other representations, and annotating records from BED or genotype information.

Why package nerds care

vcflib is package-nerd significant because it is a bag of sharp, small bioinformatics commands rather than one monolithic analysis application. Installing it adds dozens of executables whose names encode the workflow vocabulary of VCF-heavy pipelines.

It also captures a real packaging challenge in scientific software: one project ships C++ utilities, scripts, Python bindings, and library headers, and users expect it to compose with a wider command-line genomics stack across Linux, macOS, containers, and workflow systems.

Timeline

2011: VCF is introduced and described with VCFtools, establishing the ecosystem vcflib later serves.
2016-02-08: vcflib v1.0.0-rc1 appears in GitHub releases.
2019-09-03: vcflib v1.0.0 is released.
2022-05-31: The PLOS Computational Biology software paper on vcflib and related VCF tools is published.
2023: vcflib 1.0.x maintenance releases continue on GitHub.

Related projects

VCFtools is the older VCF suite and standard paper that established much of the file-format context.
bio-vcf, cyvcf2, hts-nim, and slivar are discussed with vcflib in the 2022 software paper as complementary tools for VCF processing.
FreeBayes is a related variant caller and companion project in the VCF ecosystem.
BEDTools, HTSlib, bcftools, GATK, and tabix-indexed workflows are common neighbors in pipelines that use vcflib.

Sources

security posture

Risk level: blue

broad file, network, media, or database tool signal.

Risk classifier

blue risk · medium confidence · tool

Why

broad file, network, media, or database tool signal

Signals

text:compress,sql,stream

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
`abba-baba`	executable	indexed executable	Discovered from the local executable index.
`bFst`	executable	indexed executable	Discovered from the local executable index.
`bed2region`	executable	indexed executable	Discovered from the local executable index.
`bgziptabix`	executable	indexed executable	Discovered from the local executable index.
`dumpContigsFromHeader`	executable	indexed executable	Discovered from the local executable index.
`genotypeSummary`	executable	indexed executable	Discovered from the local executable index.
`hapLrt`	executable	indexed executable	Discovered from the local executable index.
`iHS`	executable	indexed executable	Discovered from the local executable index.
`meltEHH`	executable	indexed executable	Discovered from the local executable index.
`normalize-iHS`	executable	indexed executable	Discovered from the local executable index.
`pFst`	executable	indexed executable	Discovered from the local executable index.
`pVst`	executable	indexed executable	Discovered from the local executable index.
`permuteGPAT++`	executable	indexed executable	Discovered from the local executable index.
`permuteSmooth`	executable	indexed executable	Discovered from the local executable index.
`plotHaps`	executable	indexed executable	Discovered from the local executable index.
`popStats`	executable	indexed executable	Discovered from the local executable index.
`segmentFst`	executable	indexed executable	Discovered from the local executable index.
`segmentIhs`	executable	indexed executable	Discovered from the local executable index.
`sequenceDiversity`	executable	indexed executable	Discovered from the local executable index.
`smoother`	executable	indexed executable	Discovered from the local executable index.
`vcf2bed.py`	executable	indexed executable	Discovered from the local executable index.
`vcf2dag`	executable	indexed executable	Discovered from the local executable index.
`vcf2fasta`	executable	indexed executable	Discovered from the local executable index.
`vcf2sqlite.py`	executable	indexed executable	Discovered from the local executable index.
`vcf2tsv`	executable	indexed executable	Discovered from the local executable index.
`vcf_strip_extra_headers`	executable	indexed executable	Discovered from the local executable index.
`vcfaddinfo`	executable	indexed executable	Discovered from the local executable index.
`vcfafpath`	executable	indexed executable	Discovered from the local executable index.
`vcfallelicprimitives`	executable	indexed executable	Discovered from the local executable index.
`vcfaltcount`	executable	indexed executable	Discovered from the local executable index.
`vcfannotate`	executable	indexed executable	Discovered from the local executable index.
`vcfannotategenotypes`	executable	indexed executable	Discovered from the local executable index.
`vcfbiallelic`	executable	indexed executable	Discovered from the local executable index.
`vcfbreakmulti`	executable	indexed executable	Discovered from the local executable index.
`vcfcat`	executable	indexed executable	Discovered from the local executable index.
`vcfcheck`	executable	indexed executable	Discovered from the local executable index.
`vcfclassify`	executable	indexed executable	Discovered from the local executable index.
`vcfcleancomplex`	executable	indexed executable	Discovered from the local executable index.
`vcfclearid`	executable	indexed executable	Discovered from the local executable index.
`vcfclearinfo`	executable	indexed executable	Discovered from the local executable index.
`vcfcombine`	executable	indexed executable	Discovered from the local executable index.
`vcfcommonsamples`	executable	indexed executable	Discovered from the local executable index.
`vcfcomplex`	executable	indexed executable	Discovered from the local executable index.
`vcfcountalleles`	executable	indexed executable	Discovered from the local executable index.
`vcfcreatemulti`	executable	indexed executable	Discovered from the local executable index.
`vcfdistance`	executable	indexed executable	Discovered from the local executable index.
`vcfecho`	executable	indexed executable	Discovered from the local executable index.
`vcfentropy`	executable	indexed executable	Discovered from the local executable index.
`vcfevenregions`	executable	indexed executable	Discovered from the local executable index.
`vcffilter`	executable	indexed executable	Discovered from the local executable index.
`vcffirstheader`	executable	indexed executable	Discovered from the local executable index.
`vcffixup`	executable	indexed executable	Discovered from the local executable index.
`vcfflatten`	executable	indexed executable	Discovered from the local executable index.
`vcfgeno2alleles`	executable	indexed executable	Discovered from the local executable index.
`vcfgeno2haplo`	executable	indexed executable	Discovered from the local executable index.
`vcfgenosamplenames`	executable	indexed executable	Discovered from the local executable index.
`vcfgenosummarize`	executable	indexed executable	Discovered from the local executable index.
`vcfgenotypecompare`	executable	indexed executable	Discovered from the local executable index.
`vcfgenotypes`	executable	indexed executable	Discovered from the local executable index.
`vcfglbound`	executable	indexed executable	Discovered from the local executable index.
`vcfglxgt`	executable	indexed executable	Discovered from the local executable index.
`vcfgtcompare.sh`	executable	indexed executable	Discovered from the local executable index.
`vcfhetcount`	executable	indexed executable	Discovered from the local executable index.
`vcfhethomratio`	executable	indexed executable	Discovered from the local executable index.
`vcfindelproximity`	executable	indexed executable	Discovered from the local executable index.
`vcfindels`	executable	indexed executable	Discovered from the local executable index.
`vcfindex`	executable	indexed executable	Discovered from the local executable index.
`vcfinfo2qual`	executable	indexed executable	Discovered from the local executable index.
`vcfinfosummarize`	executable	indexed executable	Discovered from the local executable index.
`vcfintersect`	executable	indexed executable	Discovered from the local executable index.
`vcfjoincalls`	executable	indexed executable	Discovered from the local executable index.
`vcfkeepgeno`	executable	indexed executable	Discovered from the local executable index.
`vcfkeepinfo`	executable	indexed executable	Discovered from the local executable index.
`vcfkeepsamples`	executable	indexed executable	Discovered from the local executable index.
`vcfld`	executable	indexed executable	Discovered from the local executable index.
`vcfleftalign`	executable	indexed executable	Discovered from the local executable index.
`vcflength`	executable	indexed executable	Discovered from the local executable index.
`vcfmultiallelic`	executable	indexed executable	Discovered from the local executable index.
`vcfmultiway`	executable	indexed executable	Discovered from the local executable index.
`vcfmultiwayscripts`	executable	indexed executable	Discovered from the local executable index.
`vcfnobiallelicsnps`	executable	indexed executable	Discovered from the local executable index.
`vcfnoindels`	executable	indexed executable	Discovered from the local executable index.
`vcfnosnps`	executable	indexed executable	Discovered from the local executable index.
`vcfnulldotslashdot`	executable	indexed executable	Discovered from the local executable index.
`vcfnullgenofields`	executable	indexed executable	Discovered from the local executable index.
`vcfnumalt`	executable	indexed executable	Discovered from the local executable index.
`vcfoverlay`	executable	indexed executable	Discovered from the local executable index.
`vcfparsealts`	executable	indexed executable	Discovered from the local executable index.
`vcfplotaltdiscrepancy.r`	executable	indexed executable	Discovered from the local executable index.
`vcfplotaltdiscrepancy.sh`	executable	indexed executable	Discovered from the local executable index.
`vcfplotsitediscrepancy.r`	executable	indexed executable	Discovered from the local executable index.
`vcfplottstv.sh`	executable	indexed executable	Discovered from the local executable index.
`vcfprimers`	executable	indexed executable	Discovered from the local executable index.
`vcfprintaltdiscrepancy.r`	executable	indexed executable	Discovered from the local executable index.
`vcfprintaltdiscrepancy.sh`	executable	indexed executable	Discovered from the local executable index.
`vcfqual2info`	executable	indexed executable	Discovered from the local executable index.
`vcfqualfilter`	executable	indexed executable	Discovered from the local executable index.
`vcfrandom`	executable	indexed executable	Discovered from the local executable index.
`vcfrandomsample`	executable	indexed executable	Discovered from the local executable index.
`vcfregionreduce`	executable	indexed executable	Discovered from the local executable index.
`vcfregionreduce_and_cut`	executable	indexed executable	Discovered from the local executable index.
`vcfregionreduce_pipe`	executable	indexed executable	Discovered from the local executable index.
`vcfregionreduce_uncompressed`	executable	indexed executable	Discovered from the local executable index.
`vcfremap`	executable	indexed executable	Discovered from the local executable index.
`vcfremoveaberrantgenotypes`	executable	indexed executable	Discovered from the local executable index.
`vcfremovenonATGC`	executable	indexed executable	Discovered from the local executable index.
`vcfremovesamples`	executable	indexed executable	Discovered from the local executable index.
`vcfroc`	executable	indexed executable	Discovered from the local executable index.
`vcfsample2info`	executable	indexed executable	Discovered from the local executable index.
`vcfsamplediff`	executable	indexed executable	Discovered from the local executable index.
`vcfsamplenames`	executable	indexed executable	Discovered from the local executable index.
`vcfsitesummarize`	executable	indexed executable	Discovered from the local executable index.
`vcfsnps`	executable	indexed executable	Discovered from the local executable index.
`vcfsort`	executable	indexed executable	Discovered from the local executable index.
`vcfstats`	executable	indexed executable	Discovered from the local executable index.
`vcfstreamsort`	executable	indexed executable	Discovered from the local executable index.
`vcfuniq`	executable	indexed executable	Discovered from the local executable index.
`vcfuniqalleles`	executable	indexed executable	Discovered from the local executable index.
`vcfvarstats`	executable	indexed executable	Discovered from the local executable index.
`vcfwave`	executable	indexed executable	Discovered from the local executable index.
`wcFst`	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 version1.0.15

manager updated2026-06-21

local dataunknown

upstreamnot available

latest detectednot detected

okNo freshness warnings were generated.

install metadata

Package metadata

Package key	brew:vcflib
Version	1.0.15
Package manager	Homebrew
Homepage	https://github.com/vcflib/vcflib
Repository	https://github.com/vcflib/vcflib
Last updated	2026-06-21T00:20:16Z
Pulse	updated
Bottle	not recorded
Service	none declared

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.

combined/vcflib.yml

Used sources

Geiger risk classifier
cross-ecosystem install command graph
curated package history
pkg.so package database
pkgdb category and tag curation