10 Call fusions with STAR-Fusion and FusionInspector

Within my pipeline I have been using two ways to detect fusions from RNA-Seq samples. They depend on whether one needs to do an exploratory or confirmatory analysis for specific fusions (requiring high sensitivity). The former analysis can be performed with STAR-Fusion and the second analysis with FusionInspector which is now integrated into STAR-Fusion as a sub module. STAR-Fusion uses the chimeric reads output from the STAR aligner to detect fusion trascripts. The wiki page of STAR-Fusion describes how to prepare all the necessary files and software requirements to run the fusion callers. These steps are also summarised in the ./functions/star_fusion_prepare.sh file and they need to be run only once. The wiki pages for both software also provide detailed information about how to interpret the results.

I created the function ./functions/star_fusion.sh which is a wrapper for STAR-Fusion.