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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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Versioning


No version available

Documentation


Maintainers


  • person_outline Niklaus Grunwald
  • person_outline Brian Knaus

Publication for vcfr

vcfr citations

 (4)
library_books

Inferring Variation in Copy Number Using High Throughput Sequencing Data in R

2018
Front Genet
PMCID: 5909048
PMID: 29706990
DOI: 10.3389/fgene.2018.00123

[…] We developed new functionality added to the current release of the vcfR package that can be used to infer copy number or ploidy in R. We initially developed vcfR for VCF data import/export, quality control, visualization and general manipulation (). vcfR now includes […]

library_books

Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics

2017
Ecol Evol
PMCID: 5792620
PMID: 29435226
DOI: 10.1002/ece3.3699

[…] well as a type of decline (one linear and two exponentials; see Table ). For each scenario, the minor allele frequencies were calculated for both Finges 1940 and 1950 populations using the R‐package vcfR (Knaus & Grünwald, ). Then, starting from the minor allele frequency distribution of Finges 1940, we simulated a new minor allele frequency distribution based on the described scenarios of popula […]

library_books

Source identification of western Oregon Douglas fir wood cores using mass spectrometry and random forest classification1

2017
Appl Plant Sci
PMCID: 5435404
PMID: 28529831
DOI: 10.3732/apps.1600158

[…] eMEAN models to identify ions that were shared by both models (Venny version 2.1; ).Finally, we generated a heat map of molecular masses and intensities for each averaged spectrum using the R package vcfR by applying a mass tolerance of 1 Da and a minimum relative abundance of 5%. Molecule relative abundance was log2 transformed to aid visualization of rare molecules. As described above, the abund […]

library_books

Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management

2017
eLife
PMCID: 5726852
PMID: 29231813
DOI: 10.7554/eLife.30925.041

[…] 7 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 alignme […]

Citations

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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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