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Add new option to fetch clinvar somatic classification + patch db for 115 #1794

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@dglemos dglemos commented Nov 18, 2024

Ticket: https://www.ebi.ac.uk/panda/jira/browse/ENSVAR-5941
Add option to return new clinvar somatic classification.

  • update dump pipeline
  • add option to vep
  • output factory to return new data types
  • patch test db
  • fix and add tests

To test this code, please point to ensembl-variation update: Ensembl/ensembl-variation#1117

@dglemos dglemos changed the title Add new option to fetch clinvar somatic classification Add new option to fetch clinvar somatic classification + patch db for 115 Nov 21, 2024
@dglemos dglemos force-pushed the add/clinvar_somatic_classification branch from cf04640 to 780862b Compare November 21, 2024 11:53
@dglemos dglemos marked this pull request as ready for review November 21, 2024 11:56
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dglemos commented Nov 21, 2024

Tests fail because of missing method get_somatic_clin_impact_by_location. This is part of this PR Ensembl/ensembl-variation#1117

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