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Clinical-Genomics / fusion-report

Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/

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fusion selection

gybeata opened this issue · comments

commented

Thank you for this stand-alone report creator it is very useful.
I have a question regarding the fusions that are reported as a separate .html. Why those? How are they selected? I have got a list of 9 .html, but only 2 of them are reported in the index.html
Also, what does the score mean in the last column of the table if index.html ?

Thank you

commented

Hi,

We are using 3 databases currently: FusionGDB, Mitelman and COSMIC. In version 1.0.0 we are only gathering data from FusionGDB, if there is no info about the fusion a page will not be generated.
This will be changed in an upcoming version. I would like to retrieve more data also from Mitelman database but I first have to figure out all the relations between the tables in the database as there is no schema anywhere.
The reason why we are using all 3 databases is that we estimate the final score from this.
Mitelman database is based on clinical studies and COSMIC is really conservative. FusionGDB looks like a good database with rich information about the fusions.

The score defines how legitimate the fusion is. It is a weighted scoring, more info can be found here.

Let me know if you have more questions 🙂