https://github.com/higlass/higlass-clinvar
Display ClinVar data in HiGlass
https://github.com/higlass/higlass-clinvar
Last synced: about 1 year ago
JSON representation
Display ClinVar data in HiGlass
- Host: GitHub
- URL: https://github.com/higlass/higlass-clinvar
- Owner: higlass
- License: mit
- Created: 2020-08-25T18:08:19.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2022-12-08T20:55:47.000Z (over 3 years ago)
- Last Synced: 2025-03-11T05:05:23.751Z (over 1 year ago)
- Language: JavaScript
- Size: 952 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# Display ClinVar variants in HiGlass
**Note**: This is the source code for the ClinVar track only! You might want to check out the following repositories as well:
- HiGlass viewer: https://github.com/higlass/higlass
- HiGlass server: https://github.com/higlass/higlass-server
- HiGlass docker: https://github.com/higlass/higlass-docker
## Installation
```
npm install higlass-clinvar
```
## Data preparation
In order to bring a ClinVar vcf file (https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/) into the required BED format, the following script can be used (make sure to adjust the file names in the script). A chrom sizes file is required.
```
python /scripts/extract_clinvar_data.py
```
The resulting bed file can be aggregated and ingested into a HiGlass server in the usual way:
```
clodius aggregate bedfile --chromsizes-filename hg38.txt --delimiter $'\t' --importance-column 6 --max-per-tile 80 clinvar_20200824.bed
python manage.py ingest_tileset --filename data/clinvar_20200824.beddb --filetype beddb --datatype bedlike --uid clinvar_20200824
```
## Usage
The live script can be found at:
- https://unpkg.com/higlass-clinvar/dist/higlass-clinvar.js
### Client
1. Load this track before the HiGlass core script. For example:
```
...
```
### Options
The following options are available:
```
{
"server": "http://localhost:8001/api/v1",
"tilesetUid": "awesome_clinvar",
"uid": "awesome_clinvar_uid",
"type": "horizontal-clinvar",
"options": {
"fontSize": 10,
"fontFamily": "Arial",
"labelTextColor": "#888888",
"levelDistance": 20, // Detemines how far the different levels are visually apart
"significanceColors": {
"pathogenic": "#ff0000",
"pathogenic_likely_pathogenic": "#ff3838",
"likely_pathogenic": "#a80000",
"uncertain_significance": "#808080",
"likely_benign": "#009600",
"benign_likely_benign": "#00c900",
"benign": "#00ff00",
"risk_factor": "#999999",
},
},
"width": 768,
"height": 200
}
```
### ECMAScript Modules (ESM)
We also build out ES modules for usage by applications who may need to import or use `higlass-clinvar` as a component.
Whenever there is a statement such as the following, assuming `higlass-clinvar` is in your node_modules folder:
```javascript
import { ClinvarTrack } from 'higlass-clinvar';
```
Then ClinvarTrack would automatically be imported from the `./es` directory (set via package.json's `"module"` value).
## Support
For questions, please either open an issue or ask on the HiGlass Slack channel at http://bit.ly/higlass-slack
## Development
### Testing
To run the test suite:
```
npm run test-watch
```
### Installation
```bash
$ git clone https://github.com/higlass/higlass-clinvar.git
$ cd higlass-clinvar
$ npm install
```
If you have a local copy of higlass, you can then run this command in the higlass-clinvar directory:
```bash
npm link higlass
```
### Commands
- **Developmental server**: `npm start`
- **Production build**: `npm run build`