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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

Allow LOMPE long read wgs uploads #3993

Open dnil opened 1 year ago

dnil commented 1 year ago

LOMPE annotates with VEP, uses svdb for freq - should be fairly doable! https://github.com/kristinebilgrav/LOMPE/

dnil commented 1 year ago

I've tested a bit with a few LOMPE files. Looks very doable on the long haul, but some modifications are needed (filed a few issues on LOMPE 😊).

We will need to add a couple of new SV-callers, Sniffles and CNVpytor.

One of the very interesting possiblities is compound calc from the long range phasing. Let's hope it works out of the box with genmod - it does have some phasing support. But we may also want to crank up the visibility of the phasing info a little regardless, and perhaps in particular accommodate display of phasing units somewhere around GT. We will typically not have the parents loaded, and while Inheritance pattern is good, it would be good to be able to check the basis for it.

We will need methylation info display as well, ideally both in text and graphics.

IGV.js is working on it: has an issue for this (https://github.com/igvteam/igv.js/issues/1650), and it is very good in the desktop app already. We could consider a separate project wrapping methylartist https://github.com/adamewing/methylartist, which is really cute.