populationgenomics / variant-curation-portal

Web application for curating loss of function variants
MIT License
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Update Django schema and frontend with new variant fields #61

Closed EddieLF closed 9 months ago

EddieLF commented 9 months ago

Tested and working in a locally hosted curation portal.

These changes will allow four new fields to be handled:

Field Description Data Type
AD Allelic depths array[array[int, int]]
AD_all Allelic depths for all ALT genotypes array[array[int, int]]
DP_all Read depths for all ALT genotypes array[int]
GQ_all Genotype quality for all ALT genotypes array[int]

The new fields have been added to the Variant Django model, the variants-schema.json relied on by the frontend, and the VariantData.js page where variant curation happens. A Django migration file has been created to modify the schema.

Example of how the new fields will appear for a variant in the input JSON:

{
        "AD": [
            [50, 47],
            [47, 48]
        ],
        "AD_all": [
            [50, 47],
            [47, 48],
            [56, 51],
            [53, 38]
        ],
        "DP_all": [127, 107, 97, 95],
        "GQ_all": [99, 99, 99, 99]
}

Here is how the variant curation page looks with the new fields: test_variant_curation_update