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 first filtered based on the ``blacklist`` from Arriba itself. Next, only fusions where at least one of the involved genes is specified in the ``report_genes`` option 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. .. csv-table:: Example input for the expression module :delim: , :file: ../../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 ------------- You can automatically generate a configuration for the fusion module using the ``utilities/create-config.py`` script. Example ^^^^^^^ .. literalinclude:: ../../test/data/config/fusion.json :language: json Configuration options ^^^^^^^^^^^^^^^^^^^^^ .. list-table:: Configuration options :widths: 30 80 15 :header-rows: 1 * - 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 - no * - cytobands - A file with cytoband information for visualization - yes * - protein_domains - A file with protein domains - yes