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Implement GKS NLJSON File Format for Somatic Variants #238

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korikuzma opened this issue Jun 19, 2024 · 0 comments
Open

Implement GKS NLJSON File Format for Somatic Variants #238

korikuzma opened this issue Jun 19, 2024 · 0 comments
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enhancement New feature or request

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@korikuzma
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Is your feature request related to a problem? Please describe.
Our team would like to use GA4GH Genomic Knowledge Standards (GKS) formatted data to submit somatic variants to ClinVar using this tool. This file format is currently not supported.

Describe the solution you'd like
I would like to add support for the GKS NLJSON file format for somatic clinical impact classification and oncogenicity classification.

@holtgrewe had said:

For integration of your use case, the next step would be to implement import from GKS NLJSON format to clinvar_api.models data (using the extra_data field for what you cannot directly import) and then implement the export.

Describe alternatives you've considered
N/A

Additional context
Here is an example of what our data looks like. Note that there may be modifications as we start implementing.

Contribution
I will be working on this issue in our fork and plan to create a PR once it's ready.

@korikuzma korikuzma added the enhancement New feature or request label Jun 19, 2024
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