I have RNA-Seq data from tumour samples and references, and I have had success calling gene fusion events. However, although I have tried a range of fusion detection tools, none of them are able to detect within-gene ('exon skipping') events such as MET ex14 skipping or EGFR vIII. I have also tried some SV callers like MANTA without any luck.
I do not want to perform differential expression / exon usage - this is just an detection exercise. Is anyone able to suggest any tools that detect exon skipping events from RNA-seq data please?