[User Story] Visualise methylation

[fellen31]

Need

As a user, I want to be able to visualise methylation. Although I'm probably not sure how.

One way would be to visualise it in IGV, either with bedMethyl or bedgraph (converted to bigWig?). Either phased, or unphased or both.
If phased, then I probably need to see phase blocks as well.

Suggested approach

• bgzip & tabix blocks.tsv from whatshap/stats #293
• Convert modkit/pileup bedMethyl to bedgraph to bigWig #294

Blockers

• Is Color alignments by base modification (5mC) supported by igv.js? igvteam/igv.js#1650

[dnil]

In principle IGV.js (main branch) supports a bedmethyl format (igvteam/igv.js#1698). I don't see a formal release with it included yet, but as soon as it should be straightforward to pass the filename to scout via the case config and we can add an IGV.js track for it.

[fellen31]

The problem with bedmethyl is I think that it doesn't say much in IGV (bottom track).

Making it into a bedgraph/bigWig is not perfect, but a bit more informative. Maybe it's a good start, if it's available in igv.js?

[dnil]

IGV has released v3(.0.1) and thus support for bedmethyl and alignment base mod flag marks: igvteam/igv.js#1698 and e.g. https://igv.org/web/release/3.0.1/examples/base-modifications.html. Scout is coming around soonish (Clinical-Genomics/scout#4724). Would you happen to have some examples around hasta?