This repository contains shell scripts to document and reproduce the analysis steps described in the manuscript Lang et al. 2024, Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates (see Figure 1B).
- The splice2neo R-package is documented here: https://github.com/TRON-Bioinformatics/splice2neo
- EasyQuant is available here: https://github.com/TRON-Bioinformatics/easyquant
- TRONflow pipelines are documented here: https://github.com/TRON-Bioinformatics/tronflow
| Step | Sub-step | Script | Comment |
|---|---|---|---|
| Mutation calling | Mapping | mutation_calling_01_mapping.sh | |
| Mutation calling | Bam pre-processing | mutation_calling_02_bam_processing.sh | |
| Mutation calling | Mutect2 | mutation_calling_03_mutect2.sh | |
| Splicing effect prediction | SpliceAI | mutation_effect_01_spliceAI.sh | example script for one sample |
| Splicing effect prediction | MMsplice | mutation_effect_02_MMsplice.sh | example script for one sample |
| Splicing detection | SplAdder | splicing_detection_01_SplAdder.sh | example script for one sample |
| Splicing detection | LeafCutter | splicing_detection_02_LeafCutter.sh | example script for one sample |
| EasyQuant | EasyQuant | easyquant.sh | example script for one sample |