The fusion module uses Arriba to call fusion events.
This module uses the bam file from STAR to call fusion events.
The fusion events are filtered based on the blacklist from Arriba itself. Also, 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.
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.
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
| Option | description | required |
|---|---|---|
genome_fasta |
Reference genome, in FASTA format | yes |
gtf |
GTF file with transcript information | yes |
blacklist |
File of blacklisted variants | yes |
known_fusions |
A file of known fusion events | yes |
report_genes |
A file of genes to report fusions for | yes |
cytobands |
A file with cytoband information | yes |
protein_domains |
A file with protein domains | yes |