Hey, what I am currently looking for is a "natural" representation of non-canonical splicing events. The problem seems to be that most spliced alignment pipelines seem to use some internal prior knowledge for assigning splice junctions. This is either a BED transcript annotation file or the pressence of a cannonical AG/GT acceptor/donor sequence in the reference. This leads wrong or missing alignments in the resulting BAM files for splice-site-mutations which introduce a new splice site, as the aligner does not have any information about the change in the DNA sequence. In the example above a new splce acceptor is generated by a germline mutation at position -12 which leads to the inclusion of 10 intronic basepairs in the new transcript. No software has yet alignet this splicing event right and called this new junction.