<img src="man/figures/logo.png" align="right" alt="logo.png" width="180" /> # The VCF Tool Box (TVTB) <!-- badges: start --> [](https://github.com/kevinrue/TVTB/actions) [](https://codecov.io/github/kevinrue/TVTB) [](https://hub.docker.com/r/kevinrue/TVTB) <!-- badges: end --> ## Bioconductor release status | Branch | R CMD check | Last updated | |:----------------:|:----------------:|:------------:| | [_devel_](http://bioconductor.org/packages/devel/bioc/html/TVTB.html) | [](http://bioconductor.org/checkResults/devel/bioc-LATEST/TVTB) |  | | [_release_](http://bioconductor.org/packages/release/bioc/html/TVTB.html) | [](http://bioconductor.org/checkResults/release/bioc-LATEST/TVTB) |  | ## Description The package provides functions to filter, summarise and visualise genetic variation data stored in VCF files. Functionalities are also demonstrated in a Shiny web-application. ## Motivation The VCF file format encodes a plethora of useful information, including optional predictions using the [Ensembl Variant Effect Predictor (VEP)](http://www.ensembl.org/info/docs/tools/vep/index.html) that can be parsed using expert packages such as [`VariantAnnotation`](https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html) and formatted into `VCF` objects. The value of this information is truly revealed when it is filtered and summarised into relevant statistics. This package offers methods: * to subset and summarise `VCF` objects including Ensembl VEP predictions, * to explore genetic variants, * and to report various summary statistics. ## Installation Instructions to install the latest release of TVTB are available at: http://bioconductor.org/packages/release/bioc/html/TVTB.html Using `devtools`, versions more recent than the official releases can be obtained: install.packages("devtools") The latest version pushed to Bioconductor [release](https://github.com/Bioconductor-mirror/TVTB/tree/release-3.4) (_may be more recent than the official release in the absence of version bump_) : devtools::install_github("Bioconductor-mirror/TVTB", ref="release-3.4") The latest version pushed to Bioconductor [devel](https://github.com/Bioconductor-mirror/TVTB/tree/master) (_as above_): devtools::install_github("Bioconductor-mirror/TVTB", ref="master") Original [GitHub](https://github.com/kevinrue/TVTB/tree/master) development repository: devtools::install_github("kevinrue/TVTB") Specific commit: devtools::install_github("kevinrue/TVTB", ref="99966dda") ## Graphical User Interface Although nothing offers more flexibility than the command line interface, a [Shiny](http://shiny.rstudio.com/) web-application, _the Shiny Variant Explorer_ (tSVE), offers a GUI to get familiar with the major functionalities of the package. ## Tests Unit tests and coverage implemented using the `testthat` package (CRAN). Coverage excludes files: * AllClasses.R (_Not executed at runtime_) * tSVE.R (_Requires interactive session_) ## License **Artistic License 2.0**