Enhance the tool to include merged=1 as a default parameter for vep_params. This will ensure that the merged Ensembl and RefSeq transcript set is used to report consequences, providing more comprehensive annotation data for human variants.
Acceptance Criteria
Modify the vep_params default to include merged=1 along with the existing defaults.
Ensure the parameter is correctly merged with user-provided vep_params.
Update tests to verify that merged=1 is included in the VEP API requests.
Update the documentation to reflect this new default parameter.
Description
Enhance the tool to include
merged=1as a default parameter forvep_params. This will ensure that the merged Ensembl and RefSeq transcript set is used to report consequences, providing more comprehensive annotation data for human variants.Acceptance Criteria
vep_paramsdefault to includemerged=1along with the existing defaults.vep_params.merged=1is included in the VEP API requests.