fusion
Tools
This module uses the bam file from STAR to call fusion events with Arriba.
The fusion events are filtered based on the blacklist from Arriba itself. Only fusions where at least one of the involved genes is in report_genes will be included in the final output.
For each fusion event that remains after filtering, we also generate a figure using the draw_fusions.R script provided by Arriba.
Input
The input for this module is a single bam file, generated by STAR per sample, specified in a PEP configuration file, as is shown [here](../test/pep/chrM-bam.csv).
Output
The output of this module are a JSON file with an overview of the most important results, as well as a number of other output files: - The final Arriba output file, after filtering. - One figure per fusion event
Configuration
Option |
Description |
Required |
genome_fasta |
Reference genome, in FASTA format |
yes |
gtf |
GTF file with transcript information |
yes |
blacklist |
File of blacklisted fusion events |
yes |
known_fusions |
A file of known fusion events |
yes |
report_genes |
Only report fusions involving genes specified in this file |
yes |
cytobands |
A file with cytoband information for visualization |
yes |
protein_domains |
A file with protein domains |
yes |