NF: let's add ViFi for viral integration

mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs

https://cmotempo.netlify.com/

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NF: let's add ViFi for viral integration #246

Open evanbiederstedt opened 5 years ago

evanbiederstedt commented 5 years ago

https://github.com/namphuon/ViFi

Docker image and Dockerfile is there.

I think this tool makes more sense than GENE-IS; we're investigating if there are differences.

evanbiederstedt commented 5 years ago

allanbolipata commented 5 years ago

Are we for sure putting this in the pipeline?

BST's reaction to adding Optitype without vetting the software gives me pause on the idea of adding things to the pipeline before we even know if the tools make sense.

evanbiederstedt commented 5 years ago

We're currently vetting it.

It seems to be a newer/better method than the GENE-IS option ClinBx uses. Bafna writes some of the best methods around. That being said, you may be right.

In this case, there is no strong experience with viral integration except for a few people in Clinical Bioinformatics. (It's also convenient that there's a Docker image with Dockerfile created by the author.)

BST's reaction to adding Optitype without vetting the software gives me pause on the idea of adding things to the pipeline before we even know if the tools make sense.

In this case, it is because the lab used HLA Polysolver already, and presented results. FWIW, I think both Optitype and Polysolver are poor methods.

allanbolipata commented 5 years ago

Sounds good!

If we do decide to put that in, can we put an example of the command used to run it here?

evanbiederstedt commented 5 years ago

Docker image here: https://hub.docker.com/r/namphuon/vifi/tags

Given they do not tag this image, I suspect we should do that. So I'll do that. If we don't use it, we can delete it.

evanbiederstedt commented 5 years ago

https://hub.docker.com/r/cmopipeline/vifi

We'll wait for Nam to version the software https://hub.docker.com/r/namphuon/vifi