Snakemake workflow: Identification of potential cancer neoepitopes from DNA-seq data
This workflow detects genomic variants with Strelka and and tries to incorporate germline and somatic variants into a sample-specific peptidome using Microphaser. Somatic neopeptides are filtered against germline peptides in terms of similarity and MHC affinity. Affinity prediction is performed using (netMHCpan, netMHC2pan). The workflow allows easy definition of tumor-normal pairs, where multiple tumor samples (e.g. metastasis) can be grouped with the same normal sample.
Software requirements
Unfortunately, the use of netMHCpan and netMHCIIpan is restricted to academic use only. To use those tools in the pipeline, please download them separately following instructions at https://services.healthtech.dtu.dk/software.php.
Please specify the path to your netMHC folder in the config.yaml.