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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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Are matching causatives looking for matchings in all categories? #4964

Open northwestwitch opened 1 week ago

northwestwitch commented 1 week ago

Like a SNV that is causative, is searched among the SVs of the case? - I can look in the code by myself as well, but I drop the question here so we remember to make sure

dnil commented 1 week ago

In case the simple id is the same, they should match: https://github.com/Clinical-Genomics/scout/blob/868323944055f899b2c5b6542c2f8da5cbbb18c0/scout/adapter/mongo/variant.py#L581

dnil commented 1 week ago

If we truly intended this as a feature, there would be a caveat for SVs having poor genotyping from at least the RD side. We do check if the matching variant was really from an affected: https://github.com/Clinical-Genomics/scout/blob/868323944055f899b2c5b6542c2f8da5cbbb18c0/scout/adapter/mongo/variant.py#L475-L504 In general the rule of matching gt is probably not fantastic for the somatic pipeline cases?

northwestwitch commented 1 week ago

n case the simple id is the same, they should match:

https://github.com/Clinical-Genomics/scout/blob/868323944055f899b2c5b6542c2f8da5cbbb18c0/scout/adapter/mongo/variant.py#L581

Let's check if the cases from that ticket if the use of causative matching would have suggested the variant among the SVs. We could use it as an argument in general when these things happen