An online tool for annotating, filtering and diagnosing patients (Exome and Genome) with Mendelian Disorders.
JavaScript HTML Python CSS PHP Shell Other
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
analyses
blog
cases
configs
dashboard
data
databases
diseases
django_select2
docs
examples
files
filter_analysis
genes
helpers
individuals
mapps
mendelmd
pagination
pathway_analysis
projects
samples
scripts
settings
static
statistics
tasks
templates
upload
variants
workers
.dockerignore
.gitignore
.travis.yml
Dockerfile
LICENSE
README.md
devlog.txt
docker-compose.yml
docker-entrypoint.sh
fabfile.py
manage.py
requirements.stable.txt
requirements.txt

README.md

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
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