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Insert some INFO data in genotype table #573

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SamuelNicaise opened this issue Jan 10, 2023 · 1 comment
Open

Insert some INFO data in genotype table #573

SamuelNicaise opened this issue Jan 10, 2023 · 1 comment
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low-priority This task shouldn't be addressed now. Fix something else before.

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@SamuelNicaise
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Some sample-related data in our pipeline ends up in INFO fields: grouped information about multiple callers (e.g. VAF list for all callers), some annotation scores, etc.

As this data is in INFO fields, it is written over everytime a new sample is inserted, as expected.
However, it turns out that some biologists want to use those annotations, and they can't anymore.

I see 3 solutions, but feel free to suggest anything else:

  1. Change our pipeline. This might be more work than changing cutevariant and all of our previous data won't fit cutevariant. Changing all the old VCFs might get tricky.

  2. Make our biologists stop using those annotations

  3. This cutevariant update so we can send the data to the genotype table when data is newly inserted:

image

@SamuelNicaise SamuelNicaise added core Cutevariant core and removed core Cutevariant core labels Jan 10, 2023
@SamuelNicaise
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We decided to go with the first solution, changing our pipeline. So this issue is now low priority for us

@SamuelNicaise SamuelNicaise added the low-priority This task shouldn't be addressed now. Fix something else before. label Apr 14, 2023
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