How to implement neoantigen sequences using WES data?

Question

[HildaJerald888]

I want to learn how to use WES to realize the whole process of neoantigen prediction, including the process and method of using BWA, Picard, Gatk and other tools in the early stage. Finally, HLA typing and the use of vep were realized.

Answer 1

[Barry Digby]

LENS: Landscape of Effective Neoantigens Software

Answer 2

[iraun]

Hi! I recommend first starting by going through the already available pipelines. Here some recommendations:

• pVAC-Seq
• MuPeXI
• nextNEOpi

But there are many more! :)