fusion locations

[jlgabre]

First off, thanks for a fast and userfriendly tool.
I have a validated fusion in my data and I'm interested in extracting in which exon the fusion/cuts occurred, i.e genomic region to see if the tool calls it successfully. It calls the gene pair, but I need specifics, how can I extract this?
The R script you provide is only on the gene level and I tried using the info provided in the json file with the start and end positions in the transcripts, by simply accumulating the exonic positions of the specific transcript to the end of the transcript, but this gives me the wrong positions, so either I'm not getting how the start and end positions in the json file should be interpreted, or the tool is not successful in identifying my fusions :-/

[janoppelt]

In case somebody finds this useful in the future - This is what I use to extract genomic coordinates of the fusion breakpoints from pizzly output. It works most of the time. I've tested this with human Ensembl GTF v102.

https://gist.github.com/janoppelt/6172dd503a54cbf5043d7ddbe947292e