Mendel,MD a user-friendly online program for clinical exome and genome analysis

Build Status BSD License Read The Docs Django

This is an online tool created to help doctors and scientists to identify disease causing variants using exome/genome sequencing data from patients with mendelian disorders.

Recently added M-CAP scores, filtering for CADD scores and Haploinsufficiency Scores.

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005520

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-16-S8-A2

Try our new test server on https://mendelmd.org Or use our original server on https://mendel.medicina.ufmg.br

OMIM Data

You need to register at OMIM: http://omim.org/downloads and submit a download request to get a file named "morbidmap.txt".

After obtaining this file you will need to put it in the folder: "data/omim/".

Installation of docker and docker-compose on Ubuntu 16.04 LTS

sudo apt-get update
sudo apt-get install software-properties-common apt-transport-https libffi-dev
sudo apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D
sudo apt-add-repository 'deb https://apt.dockerproject.org/repo ubuntu-xenial main'
sudo apt update
sudo apt-get install -y docker-engine
sudo usermod -aG docker $(whoami)
exec sudo su ${USER}
sudo curl -o /usr/local/bin/docker-compose -L "https://github.com/docker/compose/releases/download/1.11.2/docker-compose-$(uname -s)-$(uname -m)"
sudo chmod +x /usr/local/bin/docker-compose

Running Mendel,MD using Docker Compose

git clone https://github.com/raonyguimaraes/mendelmd/
cd mendelmd/
wget https://data.omim.org/downloads/addyourkeyhere/morbidmap.txt -O data/omim/morbidmap.txt
docker-compose up

Also see how to install it locally without docker-compose here:

http://mendelmd.readthedocs.io/en/latest/installation.html#manual-installation

Requirements

OR