vcfr : a package to manipulate and visualize variant call format data in R

Software to call single-nucleotide polymorphisms or related genetic variants has converged on the variant call format (VCF) as the output format of choice. This has created a need for tools to work with VCF files. While an increasing number of software exists to read VCF data, many only extract the genotypes without including the data associated with each genotype that describes its quality. We created the r package vcfr to address this issue. We developed a VCF file exploration tool implemented in the r language because r provides an interactive experience and an environment that is commonly used for genetic data analysis. Functions to read and write VCF files into r as well as functions to extract portions…

• UD
  U.S. Department of Agriculture

  Award: 5358‐22000‐039‐00D
• NI
  National Institute of Food and Agriculture

  Award: 2011‐68004‐30154