splicing_manuscript_shell_scripts

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