tbvcfreport

Generate an interactive HTML-based report from M.tb SnpEff annotated VCF(s) with links to the COMBAT-TB-eXplorer.

Usage

Prerequisites:

• SnpEff annotated M.tuberculosis VCF file(s).

Optional:

• A COMBAT-TB-NeoDB instance, tbvcfreport defaults to neodb.sanbi.ac.za.
  • See documentation if you want a local installation and export DATABASE_URI=localhost for tbvcfreport to use your local instance.

Installation

Using pip

$ pip install -i https://test.pypi.org/simple/ tbvcfreport
...

Using conda

With an activated Bioconda channel:

$ conda install tbvcfreport
...

From source

$ git clone https://github.com/COMBAT-TB/tbvcfreport.git
...
$ cd tbvcfreport
$ virtualenv envname
$ source envname/bin/activate
$ pip install -r requirements.txt
$ pip install -e .

Run tbvcfreport

$ tbvcfreport --help
Usage: tbvcfreport [OPTIONS] COMMAND [ARGS]...

  Generate an HTML-based VCF report from SnpEff annotated VCF file(s).

Options:
  --help  Show this message and exit.

Commands:
  generate  Generate an interactive HTML-based VCF report.

$ tbvcfreport generate --help
Usage: tbvcfreport generate [OPTIONS] VCF_DIR

  Generate an interactive HTML-based VCF report.

Options:
  -t, --tbprofiler-report FILENAME
                                  TBProfiler json report.
  -f, --filter-udi / -nf, --no-filter-udi
                                  Filter upstream, downstream and intergenic
                                  variants.  [default: True]
  --help                          Show this message and exit.

$ tbvcfreport generate VCF_DIR/
Processing...

This will generate a {vcf-file-name}.html file in the current working directory (pwd).

In Galaxy

We have also added tbvcfreport to the Galaxy Tool Shed.

Kindly see this repository for the latest revision.