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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Exon level coverage information #4894

Open Jakob37 opened 3 days ago

Jakob37 commented 3 days ago

I put the latest Chanjo2 in the hands of our geneticists and asked them what they would need to put this into clinical routine. It seems close to meet their needs, but they had a bunch of questions on updates to make it fully solve their situation. Let's see what you think - if reasonable or not.

Describe the solution you'd like

For incompletely covered genes / transcripts they would like to see what parts that do not reach the coverage level.

The ideal would be to be able to show for a transcript:

Would this be possible?

northwestwitch commented 3 days ago

This shouldn't be difficult to achieve. You can already create reports according to the analysis type in scout:

I guess one could add more links using variants of this form

Moving this to scout since the links to the reports are created there

northwestwitch commented 3 days ago

Regarding the (Ideally) What parts (bp positions) of these exons do not reach the coverage level request, I guess one could work on it, but it's not super easy to implement I'm afraid. And I guess watching alignments in IGV might still be more reliable in the end?

Jakob37 commented 3 days ago

Regarding the (Ideally) What parts (bp positions) of these exons do not reach the coverage level request, I guess one could work on it, but it's not super easy to implement I'm afraid. And I guess watching alignments in IGV might still be more reliable in the end?

Yes, this was just wild wishes from the geneticists. I guessed it would be hard to achieve. And not too hard to check themselves in IGV. I think we can leave that part aside.

Getting the exon coverage running though would be great 😄