An online tool for organizing, annotating, filtering and diagnosing patients with Mendelian Disorders using Exome and Genome sequencing data.


  • Python 3.4+
  • Perl 5.8+
  • Java 1.8
  • Ubuntu LTS 16.04

Other Libraries Needed


You need to register an account at OMIM: and submit a download request to get a file named “morbidmap”.

After obtaining this file you need to put it inside this folder: “mendelmd_source/data/omim/”.


Now it’s possible to install and run Mendel,MD with a single command:

docker-compose up

This command will create a container, download all the required tools, datasets and run the webserver.

This should take a few hours to complete for the first time.

Manual Installation

Installing PostgreSQL Database

sudo apt-get install libpq-dev postgresql
sudo -i -u postgres
createuser --interactive
createdb mendelmd
cp mendelmd/ mendelmd/

Installation on Ubuntu 16.04 LTS (tested)

sudo apt-get install gcc git python3-dev virtualenvwrapper zip zlibc zlib1g zlib1g-dev build-essential \
libssl-dev libffi-dev python-dev python3-dev python3-venv libcurl4-openssl-dev

python3 -m venv mendelmdenv
source mendelmdenv/bin/activate

git clone
cd mendelmd/mendelmd_source

Installing Pynnotator

pip install wheel
pip install pynnotator
pynnotator install

This will take a long time since it will download around 32GB of data. Go grab a coffee and read a paper.

Installing Mendel,MD

pip install -r requirements.txt

python migrate

wget -O data/omim/morbidmap.txt
python populate

#create yourself a super user
python createsuperuser

python runserver

And now you should have Mendel,MD running on address

Start the annotation

In another tab start the annotation process.

source mendelmdenv/bin/activate
celery -A mendelmd worker -l info -c 1

Creating a superuser

python createsuperuser

Importing Genes and Diseases Data

python populate

Upload your VCFs using the web interface

At the dashboard click on the “Upload VCF” button.

Deployment on RedHat/CentOS 7

sudo yum -y install wget
wget -O /tmp/morbidmap.txt