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Clinical-Genomics / raredisease

CG's rare disease pipeline in next flow, see the main repo here 👇
https://github.com/nf-core/raredisease
MIT License
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Add in analysis of CYP21A2? #11

Open KickiLagerstedt opened 11 months ago

KickiLagerstedt commented 11 months ago

https://www.illumina.com/science/genomics-research/articles/CYP21A2.html

dnil commented 11 months ago

Thanks, and it seems it should be in dragen 4.2, which I believe is the current official release! Unfortunately no standard core implementation yet, if I got it right? I guess we forward to nf-core/rarediseae for initial implementation, perhaps they have a good way to direct jobs specifically to dragen nodes if needed, and then we can look at good ways to display in Scout! Any preferences or suggestions there? Would you like to see copy-number only, or also fusions and the selected small variants they call?

KickiLagerstedt commented 11 months ago

We would like to see copy-number only, or also fusions and the selected small variants!

Maybe we could get our own "knapp" for this - as for SMN?

jemten commented 11 months ago

Interesting! Don't know if illumina will release a non dragen version of this tool. If not then it becomes a question if we are going the cost of dragen for our rare disease patients. We're working on adding the functionality to the new rare disease pipeline but no decision has been made of whether we will actually run it.

dnil commented 11 months ago

A lot like the HBA-tool eg, isn't it? For the CYP2D6 caller they did a regular core release as well, or perhaps rather they did that first and a dragen implementation later.

henrikstranneheim commented 11 months ago

Dragen in prod is running version 4.1.7 right now