fusion module

This module uses Arriba to call fusion genes, based on the BAM file produced in the snv-indels modules.

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 below.

Example input for the expression module
sample_name	bam
SRR8615409	test/data/bam/SRR8615409.snv-indel.bam

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

You can automatically generate a configuration for the fusion module using the utilities/create-config.py script.

Example

{
  "genome_fasta": "test/data/reference/hamlet-ref.fa",
  "gtf": "test/data/reference/hamlet-ref.gtf",
  "blacklist": "test/data/reference/arriba/blacklist_hg38_GRCh38_v2.4.0.head.tsv.gz",
  "known_fusions": "test/data/reference/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz",
  "report_genes": "utilities/deps/small-files/report_genes.txt",
  "cytobands": "utilities/deps/small-files/cytobands_hg38_GRCh38_v2.4.0.tsv",
  "protein_domains": "test/data/reference/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3"
}

Configuration options

Configuration options
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