vcfR

vcfR is an R software package to visualize and handle variant call format (VCF) data providing a link between VCF data and R. The vcfR package includes functions for reading and writing VCF data files and extracting matrices for further analyses and visualizing genomic data.

Topic

Genetic variation;Data management;Genomics

Detail

  • Operation: Formatting

  • Software interface: Library

  • Language: R

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.13.0

  • Credit: -

  • Input: <a href="https://www.internationalgenome.org/wiki/Analysis/vcf4.0" target="_blank">VCF</a>, <a href="https://en.wikipedia.org/wiki/FASTA_format" target="_blank">FASTA</a>, <a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md" target="_blank">GFF</a>

  • Output: -

  • Contact: Brian J. Knaus briank.lists@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • vcfr: a package to manipulate and visualize variant call format data in R.
  • Knaus BJ, Grünwald NJ. vcfr: a package to manipulate and visualize variant call format data in R. Mol Ecol Resour. 2017 Jan;17(1):44-53. doi: 10.1111/1755-0998.12549. Epub 2016 Jul 12. PMID: 27401132.
  • https://doi.org/10.1111/1755-0998.12549
  • PMID: 27401132
  • PMC: -
  • Inferring Variation in Copy Number Using High Throughput Sequencing Data in R.
  • Knaus BJ and Grünwald NJ. Inferring Variation in Copy Number Using High Throughput Sequencing Data in R. Inferring Variation in Copy Number Using High Throughput Sequencing Data in R. 2018; 9:123. doi: 10.3389/fgene.2018.00123
  • https://doi.org/10.3389/fgene.2018.00123
  • PMID: 29706990
  • PMC: PMC5909048

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