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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
https://cmotempo.netlify.app/
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Mutational Signatures: create a Docker image for this, and push to Dockerhub #58

Closed evanbiederstedt closed 5 years ago

kpjonsson commented 5 years ago

From this: https://github.com/mskcc/mutation-signatures

Should be run on the final somatic MAF file.

kpjonsson commented 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
evanbiederstedt commented 5 years ago

@hweej nailed it, give the guy a raise people

https://hub.docker.com/r/cmopipeline/mutation-signatures

evanbiederstedt commented 5 years ago

In psuedo-code, here’s what it does is:

  1. check to see if the maf inputted has the string ‘trinuc’ in it. If not, run the trinuc command on the maf and save the path to the outputted file
  2. run the “mutational signatures script” (main.py) on the maf with trinuc information (edited) The first command 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

kpjonsson commented 5 years ago

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.

evanbiederstedt commented 5 years ago

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