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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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Add ArtefactObs and ArtefactFrq to SNV view #4937

Open mathiasbio opened 1 month ago

mathiasbio commented 1 month ago

Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.

In the upcoming release of balsamic we are planning to add this feature: https://github.com/Clinical-Genomics/BALSAMIC/pull/1481

Which will filter variants which exist above 4 of 29 merged WGS normal samples. The tags in the info field of the VCF look as follows:

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Describe the solution you'd like

It would be nice if this information also shows up in Scout in the this variant view:

image

And here:

image

And if possible, to add a filter option as well along with the currently implemented loqusdb annotations:

image

Describe alternatives you've considered A clear and concise description of any alternative solutions or features you've considered.

Additional context Add any other context or screenshots about the feature request here.

dnil commented 1 month ago

Looks like you have a test case up there! Could you point to it here or on slack so we have a something to test with?

mathiasbio commented 1 month ago

Yes! I have 3 cases uploaded here which should have some variants annotated with this info: https://scout-stage.scilifelab.se/cust098/ such as grownshrew at position 1: 11187618