Illustrations ---------------- Fusion Diagrams ................. These are diagrams produced during the annotate step. These represent the putative fusion events of a single breakpoint pair. .. figure:: _static/GIMAP4_IL7_fusion.svg :width: 100% Fusion from transcriptome data. Intronic breakpoints here indicate retained intron sequence and a novel exon is predicted. If the :term:`draw_fusions_only` flag is set to False then all events will produce a diagram, even anti-sense fusions .. figure:: _static/UBE2V2_GIMAP4_disruptive_fusion.svg :width: 100% Disruptive Anti-sense Fusion Transcript Overlays ..................... MAVIS supports generating diagrams of all transcripts for a given gene. These can be overlaid with markers and bam_file pileup data. This is particularly useful for visualizing splice site mutations. .. figure:: _static/ENSG00000139687_RB1_overlay.png :width: 100% RB1 splice site mutation results in skipping of exon 9 The above diagram was generated using the overlay command .. code:: bash mavis overlay RB1 \ -o /path/to/output/dir \ --read_depth_plot rna /path/to/bam/file \ --marker M1 48939029 \ --annotations /path/to/mavis/annotations/reference/file