The VCF Tool Box (TVTB)
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1Latest successful build; 2Bleeding edge original GitHub repository.
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.
The VCF file format encodes a plethora of useful information,
including optional predictions using the
Ensembl Variant Effect Predictor (VEP)
that can be parsed using expert packages such as
and formatted into
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
VCFobjects including Ensembl VEP predictions,
- to explore genetic variants,
- and to report various summary statistics.
Instructions to install the latest release of TVTB are available at: http://bioconductor.org/packages/release/bioc/html/TVTB.html
devtools, versions more recent than the official releases can be
The latest version pushed to Bioconductor release (may be more recent than the official release in the absence of version bump) :
The latest version pushed to Bioconductor devel (as above):
Original GitHub development repository:
Graphical User Interface
Although nothing offers more flexibility than the command line interface, a Shiny web-application, the Shiny Variant Explorer (tSVE), offers a GUI to get familiar with the major functionalities of the package.
Unit tests and coverage implemented using the
testthat package (CRAN).
Coverage excludes files:
- AllClasses.R (Not executed at runtime)
- tSVE.R (Requires interactive session)
Artistic License 2.0