Prerequisites

Fusion detection and annotation using AGFusion

pVACfuse accepts a output directory from AGFusion as input.

AGFusion allows a user to annotate output files from several fusion callers using the agfusion batch command. The below example is for annotating the output from the STAR-Fusion caller but many other fusion callers are supported. For a full list see the AGFusion documentation.

agfusion batch \
-f <star_fusion_tsv> \
-a starfusion \
-db agfusion.homo_sapiens.87.db \
-o <output_directory> \
--middlestar \
--noncanonical

The --middlestar flag is required in order to use the ouput with pVACfuse. This will indicate the fusion position in the fusion peptide sequence.

The --noncanonical flag is optional and can be used to annotate the fusion with informations from all possible transcripts. By default only canonical transcripts are used.

Fusion detection and annotation using Arriba

Arriba detects fusions from STAR variant calls. For more information on how to run STAR and Arriba see their documentation.

Running STAR-Fusion for read support and expression information

In addition to predicting fusions, STAR-Fusion will also provide read support and expression information for the predicted fusions. The STAR-Fusion output file (either star-fusion.fusion_predictions.tsv or star-fusion.fusion_predictions.abridged.tsv) can be provided as an optional input to pVACfuse using the --starfusion-file parameter.