This can be considered the first stable release of Mendel,MD on Github.
You just need a VCF file from b37/hg19 as an input and you can start already diagnosing patients for the 4,974 Mendelian Disorders currently present at OMIM and CGD. https://www.omim.org/statistics/entry.
I now plan to create a new branch and start updating the system to work on the following next things:
- Improving the docs,
- Add JsonB support
- Add integration with GEMINI and Oncotator
- Upgrade the version of all existing libraries and tools and specially Django.
- Homomorphic Encryption of the Genomes.
Support for hg38 VCFs and CNV Analysis is coming.
Considering adding BAM/CRAM support as well.
This system was tested and deployed on Ubuntu 16.04 LTS and CentOS/RedHat 7 using PostgreSQL 9.4-9.6.
The easiest way to get it up and running is using Docker Compose command:
You can also deploy it locally using the instructions at the docs in any UNIX machine, you will need at least 60GB during installation and 30GB only at the end.