vcfr statistics

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vcfr specifications

Information


Unique identifier OMICS_19194
Name vcfr
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format VCF
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 1.8.0
Stability Stable
Requirements
methods, stats, graphics, utils, testthat, grDevices, Rcpp, dplyr, ggplot2, scales, rmarkdown, knitr, reshape2, stringr, tidyr, magrittr, R(≥3.0.1), ape, vegan, adegenet, tibble, poppr, memuse, pinfsc50, viridisLite
Source code URL https://cran.r-project.org/bin/macosx/el-capitan/contrib/3.5/vcfR_1.8.0.tgz
Maintained Yes

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Documentation


Maintainers


  • person_outline Niklaus Grunwald <>
  • person_outline Brian Knaus <>

Publication for vcfr

vcfr in publications

 (2)
PMCID: 5909048
PMID: 29706990
DOI: 10.3389/fgene.2018.00123

[…] given that empirical explorations of available data indicated that common distributions, particularly at low sequence depth, do not fit well. our method is implemented in a new update to the package vcfr in the r software environment (). r is an established and growing language facilitating the analysis of population genetic and genomic data (,). we demonstrate the utility of this method using […]

PMCID: 5726852
PMID: 29231813
DOI: 10.7554/eLife.30925.041

[…] haplotypecaller and the options ‘-erc gvcf -ploidy 1’ were used to call variants for each isolate, and the data were then combined using genotypegvcfs (). variants were filtered using the r package vcfr with depth filtering using quantile probabilities of 0.25 and 0.75 as cutoffs and a minimum of four reads, as well as a missing data cutoff of 20% (). variants were converted into a fasta […]


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vcfr institution(s)
Horticultural Crops Research Unit, USDA-ARS, Corvallis, OR, USA; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
vcfr funding source(s)
Supported in part by US Department of Agriculture (USDA) Agricultural Research Service Grant 5358-22000-039- 00D and USDA National Institute of Food and Agriculture Grant 2011-68004-30154.

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