Illustrations

Fusion Diagrams

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

Figure 2. Fusion from transcriptome data. Intronic breakpoints here indicate retained intron sequence and a novel exon is predicted.

Figure 3. Transcriptome breakpoints in the intron result in retained intron and predicts a novel exon.

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

Figure 4. 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 5. 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