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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Include genomic alteration type on the variant where available #181

Open mellybelly opened 9 years ago

mellybelly commented 9 years ago

It would be great if for each variant we were able to show the genomic alteration type, such as CNV, SNP, etc.

Others have also asked for phenotypic consequences, such as recessive, dominant, etc. as well, though this classification would be orthogonal. see https://github.com/monarch-initiative/GENO-ontology/issues/3 for consideration of these. Also these can have more complex evidence associated with them.

nlwashington commented 9 years ago

We already ingest in the sequence variant type information, typed by SO, for any of the sources that have variants. But it is not being rendered... (please enter in monarch-app).

As for the recessive vs dominant nature of the phenotypes, this seems harder. @mellybelly how would you propose going about this? I would think, if it were not called out by the data provider, it would require us to compute on the whole of the data, comparing the homo vs het phenotypes for any given locus, and compute the recessive/dominant nature? Please propose.