vcfR

1.16.0

Manipulate and Visualize VCF Data

31packages depend

136.2Kdownloads / year

68.2%test coverage

9/13checks pass

Overview

About

Maintained by Brian J. KnausFirst published 2016-02-2217 releasesCRAN page ↗GitHub ↗

Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)

install.packages("vcfR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("knausb/vcfR")

Development version from knausb/vcfR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-vcfr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-vcfR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

4NOTE9OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 8.0 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.48

68.2%

Coverage · measured lines

99%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 677 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 93%
Documented parameters: 100%
Return-value docs: 49%
References docs: 2%

Downloads

136.2K

CRAN downloads in the past year

Rank #1,455 · ~373/day · ~11.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

6.2K30 days

20.5K90 days

136.2K1 year

Compare downloads with other packages →

Also on840 r2u266.9K conda_forge535 bioconda49 c2d4u

Repository

GitHub ↗ knausb/vcfr

271Stars

54Forks

21Open issues

0Open PRs

16Releases

1,478Commits

14Contributors

vcf-datarstatsgenomicsvisualizationrcpppopulation-geneticspopulation-genomics

1,478 commits · Last activity 2026-06-08 · +0.7% stars, 30d

Stars over time

2025-07-04 · 2602026-07-13 · 271

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/knausb/vcfr on 2026-07-30.

Continuous integration (2)

GitHub ActionsAppVeyor

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.1

Imports (15)

ape dplyrgraphicsgrDevicesmagrittr memusemethodspinfsc50 Rcppstatsstringr tibbleutilsvegan viridisLite

LinkingTo (1)

Rcpp

Suggests (9)

adegenet ggplot2 knitr poppr reshape2 rmarkdown scales testthat tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

31direct

0indirect

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Brian J. Knaus

Maintainer, Author

Authors (2)

Brian J. Knaus

Maintainer, Author

Niklaus J. Grunwald

Author

Contributors (4)

Contributor

Contributor

Contributor

Contributor

Listed in earlier versions (6)

Brian J.

no longer listed · 1.0.0 to 1.16.0

Niklaus J.

no longer listed · 1.0.0 to 1.16.0

Eric C.

no longer listed · 1.1.0 to 1.16.0

David J.

no longer listed · 1.1.0 to 1.16.0

Zhian N.

no longer listed · 1.3.0 to 1.16.0

Javier F.

no longer listed · 1.6.0 to 1.16.0

Package Timeline

17 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.16.0Latest
2026-02-23 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.15.0
2023-12-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.14.0
2023-02-10 · diff ↗
1.13.0
2022-07-16 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.12.0
2020-09-01 · diff ↗
unarchivedReturned to CRAN
2020-09-01
archivedRemoved from CRAN
2020-07-05
check issues were not corrected in time
1.11.0
2020-06-05 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.10.0
2020-02-06 · diff ↗

Show 15 earlier events

1.9.0
2020-01-10 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.8.0
2018-04-17 · diff ↗
1.7.0
2018-02-08 · diff ↗
1.6.0
2017-12-08 · diff ↗
1.5.0
2017-05-18 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.4.0
2017-01-07 · diff ↗
1.3.0
2016-12-08 · diff ↗
1.2.0
2016-12-05 · diff ↗
1.1.0
2016-05-26 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.0.0
2016-02-22
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-02-22
Total releases: 17 / 10 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.1
Bundled data: 651 KB / 4 files
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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