New Analysis App!

This release adds a new 'analyses' app to enable the reproduction of genomics pipelines.

Also some changes in samples, files, and tasks apps.

New AMI

I'm creating a new AMI for Mendel,MD so I wanted to make a new point release.

Added M-CAP, CADD, Clinvar and HI Scores.

This release adds a new option to filter CADD scores, after meeting the author at ESHG he recommended 15 for recessive diseases and 25 for dominant diseases. These thresholds are currently being evaluated and should be only considered as guidance for a quick-start.

We added M-CAP scores, Haploinsufficiency scores and also Clinvar to the results of 1-Click.

New Release!

Last stable before I start updating the development branch.

Docker

Update to improve running the instance using docker-compose.

This should work much better now!

First Stable Release of Mendel,MD!

This can be considered the first stable release of Mendel,MD on Github.

You just need a VCF file as an input and you can start diagnosing patients with 4,974 Mendelian Disorders according to OMIM https://www.omim.org/statistics/entry.

I now plan to create a new branch and start updating the system to work on the following 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.

The easiest way to get it up and running is using Docker Compose command:

docker-compose up

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.