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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
https://cmotempo.netlify.app/
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Implement sigfit into NF for mutational signatures #187

Closed evanbiederstedt closed 4 years ago

evanbiederstedt commented 5 years ago

I think at the moment, we are using both Adam Abehouse's code and the sigfit code.

Refer to https://github.com/mskcc/vaporware/issues/186

kpjonsson commented 5 years ago

@evanbiederstedt What is the status of this?

evanbiederstedt commented 5 years ago

@kpjonsson I have a bit of R code which parses the column in the MAF to be used by the code. I'll throw it into Jason's container, and then we're good to go.

kpjonsson commented 5 years ago

If this is quick it can be run in the same process as the mutation-signature code. The Ref_Tri is column is added in a prior step.

evanbiederstedt commented 5 years ago

If this is quick it can be run in the same process as the mutation-signature code. The Ref_Tri is column is added in a prior step.

I think the SigFit should be a separate process after the make_trinuc step. It's a different animal, with a different docker container

evanbiederstedt commented 5 years ago

Working on this now

kpjonsson commented 5 years ago

@evanbiederstedt Status on this?

evanbiederstedt commented 5 years ago

It's depressing to admit, but this is now on the backburner until outputs finalized.

kpjonsson commented 5 years ago

Ok, no big deal in my opinion.

evanbiederstedt commented 5 years ago

....I disappointed the group, I disappointed the CMO....

but I'm really disappointed in myself :disappointed_relieved:

gongyixiao commented 4 years ago

We decided to go with @junwoo2 's https://github.com/mskcc/temposig