megSAP is a NGS data analysis pipeline for medical genetics, that is developed by the Institute of Medical Genetics and Applied Genomics and several collaborators from academia and industry. Since December 2016 the project is publically available on GitHub, however closed-source development started already in 2012.
The design goals of the project are:
- state-of-the-art in terms of sensitivity/specificity,
- fast
- and usable for diagnostics:
- we use no tools that require a license for diagnostics e.g. GATK
- extensive logging (tools, versions, parameters) ensures reproducability of results
- extensive testing before adding/updating tools or databases makes sure the results are valid
If you are interested to join the effort, please contact Marc Sturm.
- 18.01.2018: Added b-allele frequency files for visualization in IGV.
- 08.01.2018: Updated tools (BWA, samtools, snpEff) and databases (ClinVar, gnomAD, HGMD).
- 15.12.2017: Added runs-of-homozygosity detection to the germline pipeline.
There are no releases yet.
Please use git to download the most recent development version:
git clone --recursive https://github.com/imgag/megSAP.git
If you are behind a proxy that block the standard git port, you see something like this:
$ git clone --recursive https://github.com/imgag/megSAP.git
Cloning into 'megSAP'...
fatal: Unable to look up github.com (port 9418) (Name or service not known)
Then you have to adapt your ~/.gitconfig file like that:
[http]
proxy = http://[user]:[password]@[host]:[port]
megSAP (or one of the used tools) depends mainly on the following software to be installed:
- g++ (4.5 or higher)
- qmake (Qt 5.5 or higher, including xmlpatterns and mysql package)
- git
- cmake
- python (including matplotlib)
- php
- tabix
- java
For example, the installation of the dependencies using Ubuntu 16.04 looks like that:
> sudo apt-get install -y wget bzip2 unzip make g++ git cmake tabix build-essential qt5-default qt5-qmake qtbase5-dev libqt5sql5-mysql libqt5xmlpatterns5-dev php7.0-cli php7.0-xml php7.0-mysql python python-matplotlib libncurses5-dev bzip2 libbz2-dev liblzma-dev default-java
First, we need to download the tools the pipeline relies on:
> cd megSAP/data/
> chmod 755 download_*.sh
> ./download_tools.sh
Next, we need to download and index the reference genome:
> ./download_GRCh37.sh
Finally, we need to download and convert some open-source databases for annotations:
> ./download_dbs.sh
Note: OMIM, HGMD and COSMIC are not downloaded automatically because of license issues. If you have the license for those databases, download/convert them according to the commented sections in the download script.
Documentation about the different analysis pipelines can be found here:
- DNA analysis (single sample)
- DNA analysis (multi-sample and trio)
- DNA analysis (tumor-normal pair)
- RNA analysis (expression)
- RNA analysis (variant calling) - coming soon
Please report any issues or questions to the megSAP issue tracker.