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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
- Documentation: https://cran.r-project.org/web/packages/vcfR/vcfR.pdf
Maintainers
- person_outline Niklaus Grunwald <>
- person_outline Brian Knaus <>
Publication for vcfr
vcfr in publications
(2)[…] 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 […]
Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management
[…] 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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