bio-workflows-neoantigen-pipeline

Step 1: HLA Typing (if not provided)

HLA types are critical for MHC binding prediction. If not already known from clinical testing:

## Parse results

cat hla_output/tumor.genotype.json
python
import json

with open('hla_output/tumor.genotype.json') as f:
    hla_data = json.load(f)

hla_alleles = []
for gene, alleles in hla_data.items():
    for allele in alleles:
        hla_alleles.append(f'HLA-{allele}')

## Format for pVACseq: HLA-A*02:01,HLA-A*24:02,HLA-B*07:02,...

hla_string = ','.join(hla_alleles)
print(f'HLA alleles: {hla_string}')