Fig. 2

Overview of the SwissMTB bioinformatics analysis workflow. The reads generated by the sequencer are first mapped to the human reference genome. Afterwards, somatic variant and copy number variant calling is performed. Variants are annotated and then prioritized according to clinical relevance. RNA-seq based gene expression levels are compared to publicly available tumor sample cohorts. The findings are summarized in a clinical report. All steps from mapping to prioritization are fully automatized using a Snakemake-based pipeline. Selecting variants and therapies for the report is currently mainly manual work. All steps are documented and quality controlled, partly based on built-in routines in the analysis pipelines