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VariED

The website is freely available at http://varied.cgm.ntu.edu.tw/
VariED is a web-based querying system with an integrated annotation database and expression profiles for human genetic variants. The system was written in Python with Flask framework.
VariED is under the VariED project in Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine.

Getting Started

Requirements

  • Git
  • Python 3.4+
  • Flask 0.10.1
  • ANNOVAR
  • CADD

Set up a Python Virtual Environment

Built-in venv

Create the virtual environment at <repo>/venv:

python3 -m venv venv

To activate it:

. venv/bin/activate

Install Dependencies

Use pip:

pip install -r requirements.txt

Set up Local Environment Variables

Edit the 'Path' in VariED.py

Run server

python project/VariED.py

Databases

Please contact dytk2134[at]gmail[dot]com to let me know if need to get the data in VariED. For large files, we will provide FTP for you:)