Neoantigens provide a promising source for targeting cancer cells through targeted re-activation of immune cells. However, identifying neoantigens is a challenging task due to their low abundance and cancer heterogeneity. We have developed a proteogenomics pipeline which takes processed sequencing (RNA, DNA) data and proteomics data from matching human clinical samples as inputs, and uses the sequences to find unconventional mutant peptides in the proteomics data. Prior to running this pipeline on normal infrastructure, sequencing data must be processed in order to create sequences of non-sensitive somatic cancer mutations. This part we aim to run on Bianca.