Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
152 stars 46 forks source link

Ribbon/SplitThreader integration #4877

Open dnil opened 1 month ago

dnil commented 1 month ago

Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.

Ribbon https://github.com/MariaNattestad/Ribbon appears to be a customer enjoyed SV viz program, especially on the LRS side, although it does support SR as well. They used to only work with some bespoke bedpe thingy, but have a new release since of a few weeks integrating VCF support. It is apparently actively maintained, pretty and probably a lighter tonic to instruct use of than switching back and forth between IGV.js and the SV list view.

Describe the solution you'd like Integrate a Ribbon view on SVs. This would involve preparing a "session" json, much like the js config for IGV.js, setting URLs of different resource files to serve (bam, vcf, coverage bed), and giving a locus to start the view in the URI as get options https://github.com/MariaNattestad/Ribbon/blob/main/docs/release_notes_v2.md#specify-a-locus-in-the-url.

Additional context This is a bit exploratory still, so before we go full implementation, lets pilot a bit and see that there are no major showstoppers we missed.

dnil commented 1 month ago