Whether germline mutation data is needed to correct neoantigen identified by somatic mutation data？
I got the patient's somatic mutation data through the GATK toolkit. I plan to use the pVACseq tool to get the predicted neoantigen. However, the pVACseq tool requires the patient's germline mutation data. The explanation given by the pVACseq tool developers is that germline mutations that are close to somatic mutations may affect mutant peptides calculated from somatic mutations.
My question is whether germline mutation data is necessary for neoantigen predictions?