OncoKB Annotation Module¶

Overview¶

The OncoKB module annotates somatic variants using the OncoKB MAF Annotator to obtain clinically actionable variant-drug associations.

How It Works¶

Input MAF file is processed under the GRCh38 reference genome
Cancer type is specified for disease-specific evidence levels
The annotator queries the OncoKB API for each variant
Output includes oncogenicity, actionability levels, and drug associations

Key Output Fields¶

Field	Description
`ONCOGENIC`	Oncogenicity classification
`HIGHEST_LEVEL`	Highest therapeutic evidence level
`VARIANT_IN_ONCOKB`	Whether the variant exists in OncoKB
`Drugs`	Associated drug names
`oncokb_level`	Evidence level (1, 2, 3A, 3B, 4, R1, R2)
`oncokb_score`	Numeric score mapped from evidence level

API Token¶

An OncoKB API token is required. Request one at oncokb.org/api-access (free for research use).

Usage¶

from oncokb_module import run_oncokb_and_extract

oncokb_df = run_oncokb_and_extract(
    maf_path="sample.maf",
    cancer_type="Non-Small Cell Lung Cancer",
    output_tsv_path="oncokb_output.tsv",
    annotator_path="/path/to/MafAnnotator.py",
    oncokb_api_token="YOUR_TOKEN"
)