vcfR documentation

Brian J. Knaus and Niklaus J. Grünwald

The R package vcfR is a set of tools designed to read, write, manipulate and analyze VCF data.

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.

vcfR on CRAN.
vcfR on GitHub.

GitHub site for vcfR_documentation.


Knaus, Brian J., and Niklaus J. Grunwald. 2017. VCFR: a package to manipulate and visualize variant call format data in R. Molecular Ecology Resources 17(1):44-53.

Knaus, Brian J., and Niklaus J. Grunwald. 2016. VcfR: an R package to manipulate and visualize VCF format data. bioRxiv: 041277.

Copyright © 2017, 2018 Brian J. Knaus. All rights reserved.

USDA Agricultural Research Service, Horticultural Crops Research Lab.