consider arriba visualization

[anoronh4]

singularity image we are using for arriba also contains /usr/local/bin/draw_fusions.R. We might consider to use this script to add a visualization output for fusions that are found by arriba.

[andref1989]

I have written some code for visualizing the reads from a fusion set reported by arriba if you're interested. It's based on a few R-based packages but it's not quite perfect yet with a lot of room for optimization that I can share if interested.

[anoronh4]

thanks for showing this! we discussed visualization recently and made a couple of decisions:

1. we are thinking that this is a low priority because every analyst will likely want to do their own visualization based on their needs
2. if we do produce some sort of visualization, it should be based off the merged fusion result rather than from a specific caller.
3. visualization might be a bit pre-mature because we are still deciding how the final fusions will be merged/presented.

do you think that your code can be easily adapted for different formats of fusion calls? what are the necessary pieces of information to run it?

[andref1989]

This visualization uses the final merged and/or arriba fusion calls in the same format as it currently exists in the pipeline. It can handle bedpe formats without much difficulty either.

For plotting the fusions as is, I only need the bam file and the list of fusions.

[anoronh4]

This sounds like it would integrate pretty well! I think once we have figured out how final fusions will be merged/presented, that would be a good time to start putting it in. To implement we'd need a) a docker/singularity container with all necessary packages/softwares and b) a copy of the custom script(s) to maintain within the repo. If we could work on having those ready by then that would be awesome!

[andref1989]

I'll try to put those together!