Illustrations¶

Fusion Diagrams¶

These are diagrams produced during the annotate step. These represent the putative fusion events of a single breakpoint pair.

Figure 27. Fusion from transcriptome data. Intronic breakpoints here indicate retained intron sequence and a novel exon is predicted.¶

If the draw_fusions_only flag is set to False then all events will produce a diagram, even anti-sense fusions

_images/UBE2V2_GIMAP4_disruptive_fusion.svg

Figure 28. 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 29. RB1 splice site mutation results in skipping of exon 9¶

The above diagram was generated using the overlay command

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