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4) Evidence based Reciprocal annotation filter: data can be filtered according to the presence of reciprocal translocation (there should be evidence of the fusion transcript and of its reciprocal) evidence. It is often useful to discriminate between balanced reciprocal translocations and read-through fusions.
5) Score threshold: data can be filtered according to a user defined threshold score.
6) Evidence based Strand annotation filter: the two fusion partners must be ‘strand compatible’ to produce functional fusions.
7) Evidence based Frame annotation filter: all the candidate fusions where the two partners aren’t able to generate in frame transcripts are filtered out. The application of this filter requires the identification of a valid breakpoint junction and thus it’s only applicable to those candidates that are ‘Junction annotation’ positive.
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