| !!! NOTE: This is the GRCh38 version. If you want to use the old GRCh37 version, use the branch!!! |
|---|
megSAP is a NGS data analysis pipeline for medical genetics, which is developed by the Institute of Medical Genetics and Applied Genomics and several collaborators from academia and industry. Since December 2016 the project is publicly 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
- 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.
The installation of megSAP is quite time-consuming because many tools and big databases need to installed.
The installation instructions can be found here.
Documentation about the different analysis pipelines can be found here:
- DNA germline analysis (single sample)
- DNA germline analysis (multi-sample and trio)
- DNA somatic analysis (tumor-normal pair / tumor only)
- RNA analysis (expression)
Please report any issues or questions to the megSAP issue tracker.
- 13.01.2021 Removed dbscSNV and MMsplice annotations since they are not used.
- 05.01.2021 Added gnomAD AF annotation of mitochondrial variants (#107).
- 04.01.2021 Fixed missing CNV calls for chromosome ends (mainly chr17, chr18, chr20 and chrX).
- 22.12.2021 Updated all databases except RNA-only databases
- 22.11.2021 GRCh38 is now the default. The GRCh37 version is availailable through the respective branch now.
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent