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https://github.com/combat-tb/tbvcfreport
Generate an interactive HTML-based report from M.tb SnpEff annotated VCF(s)
https://github.com/combat-tb/tbvcfreport
combat-tb-neodb galaxy-project neo4j snpeff tuberculosis variant-annotations vcf vcf-files
Last synced: 4 months ago
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Generate an interactive HTML-based report from M.tb SnpEff annotated VCF(s)
- Host: GitHub
- URL: https://github.com/combat-tb/tbvcfreport
- Owner: COMBAT-TB
- License: gpl-3.0
- Created: 2018-03-05T10:22:48.000Z (almost 7 years ago)
- Default Branch: main
- Last Pushed: 2024-06-07T11:02:56.000Z (8 months ago)
- Last Synced: 2024-10-11T04:42:02.270Z (4 months ago)
- Topics: combat-tb-neodb, galaxy-project, neo4j, snpeff, tuberculosis, variant-annotations, vcf, vcf-files
- Language: Python
- Homepage:
- Size: 1.34 MB
- Stars: 2
- Watchers: 4
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# **tbvcfreport**
[](http://bioconda.github.io/recipes/tbvcfreport/README.html)
Generate an interactive HTML-based report from *M.tb* SnpEff annotated VCF(s) with links to the [COMBAT-TB-eXplorer](https://explorer.sanbi.ac.za/).
## Usage
**Prerequisites:**
- [SnpEff](http://snpeff.sourceforge.net/SnpEff_manual.html) annotated *M.tuberculosis* VCF file(s).
**Optional:**
- A [COMBAT-TB-NeoDB](https://github.com/COMBAT-TB/combat-tb-neodb) instance, `tbvcfreport` defaults to [neodb.sanbi.ac.za](https://neodb.sanbi.ac.za).
- See [documentation](https://github.com/COMBAT-TB/combat-tb-neodb) if you want a local installation and `export DATABASE_URI=localhost` for `tbvcfreport` to use your local instance.
### Installation
#### Using `pip`
```sh
$ pip install -i https://test.pypi.org/simple/ tbvcfreport
...
```
#### Using `conda`
With an activated [Bioconda](https://bioconda.github.io/) channel:
```sh
$ conda install tbvcfreport
...
```
#### From source
```sh
$ 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`
```sh
$ 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.
```
```sh
$ 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.
```
```sh
$ 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](https://github.com/galaxyproject) [Tool Shed](https://toolshed.g2.bx.psu.edu/repository?repository_id=47a4512ab5a77049).
Kindly see [`this repository`](https://toolshed.g2.bx.psu.edu/repository?repository_id=47a4512ab5a77049) for the latest revision.
