Closed evanbiederstedt closed 5 years ago
To be specific:
python make_trinuc_maf.py input.maf input.trinuc.maf && \
python main.py Stratton_signatures30.txt input.trinuc.maf input.mutsig.txt
@hweej nailed it, give the guy a raise people
In psuedo-code, here’s what it does is:
python make_trinuc_maf.py 'path/to/maf' 'path/to/output/maf/withTrinuc'
The output is:
'path/to/output/maf/withTrinuc'
The second command is python main.py 'path/to/Stratton_signatures30.txt' 'path/to/maf/annotated/withTrinuc' 'path/to/output'
I suggest we ignore the --spectrum
and --spectrum_output
EDIT: MAFs output from the pipeline always need to be processed through python make_trinuc_maf.py
More precisely, the make_trinuc_maf.py
script adds the column Ref_Tri
to the MAF and that is the column the main.py
script uses.
More precisely, the make_trinuc_maf.py script adds the column Ref_Tri to the MAF and that is the column the main.py script uses.
Right! I should also clarify that the MAFs output from the pipeline always need to be processed through python make_trinuc_maf.py
From this: https://github.com/mskcc/mutation-signatures
Should be run on the final somatic MAF file.