Mendel,MD a user-friendly online program for clinical exome and genome analysis
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
- At least 60GB of disk space
- Python 3.4+
- Perl 5.8+
- Java 1.8
- Ubuntu LTS 16.04/CentOS 7 or Red Hat 7
OR
- Docker
- Docker Compose