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VcfR: a package to manipulate and visualize VCF format data in R

View ORCID ProfileBrian J. Knaus, View ORCID ProfileNiklaus J. Grünwald
doi: https://doi.org/10.1101/041277
Brian J. Knaus
1Horticultural Crops Research Unit, USDA-ARS, Corvallis, 97330, USA
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Niklaus J. Grünwald
1Horticultural Crops Research Unit, USDA-ARS, Corvallis, 97330, USA
2Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
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Abstract

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 of the data and to plot summary statistics of the data are implemented. VcfR further provides the ability to visualize how various parameterizations of the data affect the results. Additional tools are included to integrate sequence (FASTA) and annotation data (GFF) for visualization of genomic regions such as chromosomes. Conversion functions translate data from the vcfR data structure to formats used by other R genetics packages. Computationally intensive functions are implemented in C++ to improve performance. Use of these tools is intended to facilitate VCF data exploration, including intuitive methods for data quality control and easy export to other R packages for further analysis. VcfR thus provides essential, novel tools currently not available in R.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 26, 2016.
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VcfR: a package to manipulate and visualize VCF format data in R
Brian J. Knaus, Niklaus J. Grünwald
bioRxiv 041277; doi: https://doi.org/10.1101/041277
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VcfR: a package to manipulate and visualize VCF format data in R
Brian J. Knaus, Niklaus J. Grünwald
bioRxiv 041277; doi: https://doi.org/10.1101/041277

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