Work on mutation ETL - Githubissues

monarch-initiative / oncoexporter

Cancer data to GA4GH phenopacket

https://monarch-initiative.github.io/oncoexporter

MIT License

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Work on mutation ETL #73

Closed ielis closed 5 months ago

ielis commented 5 months ago

Enhance ETL of the mutation table into Phenopacket Schema's VariantInterpretation elements in CdaMutationFactory.

The PR includes several changes:

add few more checks to the previously used VariantInterpretation fields
do not include an HGVS expression if transcript ID is missing to prevent ambiguity/inconsistency
do not create a VCF record for ref/mut alleles that include dashes - (see #72 )
create an VariationDescriptor.id by hashing all row fields
store tumor/normal read counts in extensions
store mutation status in an extension