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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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Support CIViC annotation for somatic mutations #4968

Open muabnezor opened 1 week ago

muabnezor commented 1 week ago

CIViC (Clinical Interpretation of Variants in Cancer) is an open-access, community-driven resource for the clinical interpretation of cancer variants. To enhance Scout’s functionality for somatic variants, it would be beneficial to see this information in scout.

One way to achieve this would before loading the variants into scout annotate the vcf against the CIViC database, and add support in scout to load the relevant civic annotations into scout.

dnil commented 1 week ago

If you have a VCF with CiViC annotations and a key for those this should be really simple and useful! Perfect!

Do they provide a VEP plugin or annotation track for use perhaps?

As I'm sure you know, Scout has a CiViC gene level linkout - that was the API level we were comfortable with last time this was on the table.

Screenshot 2024-10-18 at 15 29 59

dnil commented 1 week ago

If their API has matured to allow confident variant lookups (eg using transcript qualifiers for aa changes) we can also make a variant level linkout, but I get the feeling this is still a bit rough around the edges?

muabnezor commented 1 week ago

Hi, no currently no vep plugin, so this is something that needs to be solved. I have started looking at this https://docs.civicpy.org/en/latest/, but have not yet tested it. But yes this will be a matter of first confidently annotate variants, before submitting loading them to scout.