cellink.tl.add_vep_annos_to_gdata#
- cellink.tl.add_vep_annos_to_gdata(vep_anno_file, gdata, id_col_vep='#Uploaded_variation', cols_to_drop=None, dummy_consequence=True)#
Add VEP annotations to a gdata object.
- Parameters:
vep_anno_file (str) – Path to the VEP annotation file (e.g., output from run_vep).
gdata (object) – Object representing genomic data to which the annotations will be added.
id_col_vep (str) – Column name in the VEP file used for variant IDs, by default “#Uploaded_variation”.
cols_to_drop (list) – List of columns to drop from the annotations, by default [“Allele”, “Feature_type”, “Location”].
dummy_consequence (bool) – If True, one-hot encodes the “Consequence” column into multiple binary columns, by default True.
- Return type:
- Returns:
object The updated gdata object with VEP annotations added as
uns["annotation_vep"].