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
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 flag is required in order to use the ouput with pVACfuse.
This will indicate the fusion position in the fusion peptide sequence.
--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
star-fusion.fusion_predictions.abridged.tsv) can be provided as an
optional input to pVACfuse using the