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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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translocated to different chromosomes #247

Closed liu3c closed 1 month ago

liu3c commented 2 months ago

Dear @mnshgl0110

Is it normal to identify translocation variants in multiple samples that are in the same reference genome coordinates but translocated to different chromosomes? For example, some samples transpose to Chr10 and others to Chr2 How can I fix it? Thanks for your time and help. best regards.

mnshgl0110 commented 2 months ago

Yes, it is possible to find such translocations, specially for transposable elements. It is unclear to me why you need to fix it? And what would be the "fixed" output?

liu3c commented 2 months ago

Thank you for your reply, I mean is such a variant not being used as a translocation, does it need to be removed?

mnshgl0110 commented 2 months ago

Sorry, I am unable to understand the question. Can you please share some more information, and maybe some examples?