vcfR | Tools to work with variant call format files | Genomics library

vcfR is a R library typically used in Artificial Intelligence, Genomics applications. vcfR has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

VcfR is an R package intended to allow easy manipulation and visualization 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 from the VCF data for use with typical R functions. 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 or converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and the R environment connecting familiar software with genomic data. VcfR is built upon two data structures. vcfR - S4 class to contain data from a VCF file. chromR - S4 class to contain variant information (VCF) and optional sequence (FASTA) and annotation (GFF) information. Functions in vcfR provide the ability to subset VCF data as well as to extract and parse the data. For example, individual genotypes, sequence depths or genotype likelihoods (when provided in the VCF file) can easily be accessed. These tools are provided to aid researchers in rapidly surveying the quality and other characteristics of data provided as VCF data. With this information in hand, researchers should be able to determine criteria for hard filtering in order to attempt to maximize biological variation and minimize technical variation.