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<p>
<center>
<h3>vcfR documentation</h3>
by
<br>
Brian J. Knaus and Niklaus J. Grünwald
</center>
</p>
<div id="header">
<h1 class="title toc-ignore">vcfR: VCF data in R</h1>
</div>
<p>The R package vcfR is a set of tools designed to read, write,
manipulate and analyze VCF data.</p>
<p>Facilitates easy manipulation of <a
href="https://github.com/samtools/hts-specs">variant call format
(VCF)</a> 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 of data. 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
(*.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 R
software.</p>
<p><a href="https://CRAN.R-project.org/package=vcfR">vcfR</a> on
CRAN.<br />
<a href="https://github.com/knausb/vcfR">vcfR</a> on GitHub.</p>
<p>GitHub site for <a
href="https://github.com/knausb/vcfR_documentation">vcfR_documentation</a>.</p>
<hr />
<div id="publication" class="section level2">
<h2>Publication</h2>
<p>Knaus, Brian J., and Niklaus J. Grunwald. 2017. VCFR: a package to
manipulate and visualize variant call format data in R. Molecular
Ecology Resources 17(1):44-53. <a
href="http://dx.doi.org/10.1111/1755-0998.12549"
class="uri">http://dx.doi.org/10.1111/1755-0998.12549</a>.</p>
<p>Knaus, Brian J., and Niklaus J. Grunwald. 2016. VcfR: an R package to
manipulate and visualize VCF format data. bioRxiv: 041277. <a
href="http://dx.doi.org/10.1101/041277"
class="uri">http://dx.doi.org/10.1101/041277</a>.</p>
</div>
<center>
<hr class="style1">
<p>Copyright © 2017, 2018 Brian J. Knaus. All rights reserved.</p>
<p>USDA Agricultural Research Service, Horticultural Crops Research Lab.</p>
</center>
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