Parses SnpEff generated VCF and generates an HTML report.
Project description
tbvcfreport
A tool to generate an interactive HTML-based report from SnpEff annotated VCF file(s) with links to the Combat-TB-Explorer.
Usage
Prerequisites:
python-pip
- SnpEff annotated M.tuberculosis VCF file(s).
- A Combat-TB-NeoDB instance,
tbvcfreport
defaults to neodb.sanbi.ac.za.- See combat-tb-neodb if you want a local installation and
export DATABASE_URI=localhost
fortbvcfreport
to use your local instance.
- See combat-tb-neodb if you want a local installation and
Installation
Using pip
$ pip install -i https://test.pypi.org/simple/ 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
:construction:
We have also added tbvcfreport
to the Galaxy Test Tool Shed.
Kindly see this repository
for the latest revision.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
tbvcfreport-0.1.7.tar.gz
(12.1 kB
view hashes)