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Add ArtefactObs and ArtefactFrq to SNV view #4937

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mathiasbio opened this issue Oct 14, 2024 · 2 comments
Open

Add ArtefactObs and ArtefactFrq to SNV view #4937

mathiasbio opened this issue Oct 14, 2024 · 2 comments

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@mathiasbio
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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: Clinical-Genomics/BALSAMIC#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:

image

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
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dnil commented Oct 14, 2024

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
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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

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