README.md

In TVTB: TVTB: The VCF Tool Box

The VCF Tool Box (TVTB)

Software status

| Platforms | OS | R CMD check | Coverage1 | |:----------------:|:----------------:|:----------------:|:----------------:| | AppVeyor2 | Windows | | N/A | | Travis CI2 | Linux | | | | Bioc (devel) | Multiple | | NA | | Bioc (release) | Multiple | | NA |

1Latest successful build; 2Bleeding edge original GitHub repository.

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) that can be parsed using expert packages such as VariantAnnotation 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 (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 (as above):

devtools::install_github("Bioconductor-mirror/TVTB", ref="master")

Original GitHub 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 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

TVTB documentation built on Nov. 8, 2020, 6:09 p.m.