combat-tb / tbvcfreport

Generate an interactive HTML-based report from M.tb SnpEff annotated VCF(s)

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.

tbvcfreport's Issues

Add HGVS.p as Consequence

HGVS.p: If variant is coding, this field describes the variant using HGVS notation (Protein level).

Indicate if variant is known

Might be useful to indicate if the variant was mentioned. Possible sources:

• TBProfiler

• Miotto, et al. (2017)