The R package vcfR is a set of tools designed to read, write,manipulate and analyze VCF data.
Facilitates easy manipulation ofvariant call format(VCF) data. Functions are provided to rapidly read from and write toVCF files. Once VCF data is read into R a parser function extractsmatrices of data. This information can then be used for quality controlor other purposes. Additional functions provide visualization of genomicdata. 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 Rsoftware.
GitHub site forvcfR_documentation.
Knaus, Brian J., and Niklaus J. Grunwald. 2017. VCFR: a package tomanipulate and visualize variant call format data in R. MolecularEcology Resources 17(1):44-53.http://dx.doi.org/10.1111/1755-0998.12549.
Knaus, Brian J., and Niklaus J. Grunwald. 2016. VcfR: an R package tomanipulate and visualize VCF format data. bioRxiv: 041277.http://dx.doi.org/10.1101/041277.
Copyright © 2017, 2018 Brian J. Knaus. All rights reserved.
USDA Agricultural Research Service, Horticultural Crops Research Lab.