Integrative mutational signature portal (MsigPortal) for cancer genomic study
Here are some basic steps:
- Download the script and three Packages from Github:
https://github.com/xtmgah/SigProfilerPlotting
https://github.com/xtmgah/SigProfilerMatrixGenerator
https://github.com/xtmgah/SigProfilerClusters
https://github.com/xtmgah/mSigPortal
- Install them locally based on the following order:
pip install -e Path/SigProfilerClusters-master/
pip install -e Path/SigProfilerPlotting-master/
pip install -e Path/SigProfilerMatrixGenerator-master/
- Download Reference Genome, e.g.,'GRCh37’
$ python
from SigProfilerMatrixGenerator import install as genInstall
genInstall.install('GRCh37', rsync=False, bash=True)
genInstall.install('GRCh38', rsync=False, bash=True)
- Run Script: python3 mSigPortal_Profiler_Extraction.py -f vcf -i Demo_input_Test/demo_input_multi.vcf.gz -p Project -o test-15 -g GRCh37 -t WGS -C True