As a Lancet user, I will have some Lancet output (or some variants from another source). I have a list of called variants, and I want to inspect my calls and the sample reads on the tube map.
There should be a worked tutorial or some other good documentation about how I can get my whole list of variants into a nice Tube Map BED file that I can view on the tube map (probably on the official deployment).
This might look like a polished version of the wrapper loop around the subgraph chunk generation script, committed to the repo, and a Markdown tutorial with screenshots that covers running it, hosting the resulting files somewhere, and loading it up.
This could start with Lancet GFAs and a big BAM and cover pulling the reads and Giraffe-ing them.
It would be good to also have a way in from a VCF here: construct graphs at each variant, pull reads from a BAM, realign with Giraffe, and turn into a tube map BED of examples.
We might consider having the script here drive Lancet, unless Lancet has its own driver script.
As a Lancet user, I will have some Lancet output (or some variants from another source). I have a list of called variants, and I want to inspect my calls and the sample reads on the tube map.
There should be a worked tutorial or some other good documentation about how I can get my whole list of variants into a nice Tube Map BED file that I can view on the tube map (probably on the official deployment).
This might look like a polished version of the wrapper loop around the subgraph chunk generation script, committed to the repo, and a Markdown tutorial with screenshots that covers running it, hosting the resulting files somewhere, and loading it up.
This could start with Lancet GFAs and a big BAM and cover pulling the reads and Giraffe-ing them.
It would be good to also have a way in from a VCF here: construct graphs at each variant, pull reads from a BAM, realign with Giraffe, and turn into a tube map BED of examples.
We might consider having the script here drive Lancet, unless Lancet has its own driver script.