prediction effect for in frame ins/del

Clinical-Genomics / scout

VCF visualization interface

https://clinical-genomics.github.io/scout

BSD 3-Clause "New" or "Revised" License

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prediction effect for in frame ins/del #333

Closed 4WGH closed 5 years ago

4WGH commented 7 years ago

could this be implemented in SCout? See publication link This would complement the severity prediciton when SIFT and polyphen can not

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077940

moonso commented 7 years ago

Think that this is a question for @henrikstranneheim if it should be included in MIP

moonso commented 7 years ago

Please have a look at that @henrikstranneheim

dnil commented 7 years ago

It operates with the at first sight counterintuitive result that changes to repeat stretches are likely to affect function. Unless in an unordered part of the protein. Interesting!

dnil commented 7 years ago

Fig 3 reconciles the world views: one-aa changes to a e.g. a polyQ is not so likely to be disease-causing, but two much more so.

4WGH commented 5 years ago

question about prediction of in frame deletion come up again. something to look into?

dnil commented 5 years ago

One version seen operational in Lund; Paul P has a working setup running CADD locally on indels - I'm sure he would help iron out any issues we may run into there. SIFT Indel looks nice enough, but CADD seems like a great place to start.

henrikstranneheim commented 5 years ago

IN MIP decided to:

Skip SIFT locally for indels as it is not practical to implement in a production setting and will most likely add less than CADD.
Added dynamic calculation of CADD for indels. VCF key "CADD" as usual.

dnil commented 5 years ago

Ok, if the keys are as for regular SNVs, we simply close this issue! Thank you - this should be helpful! :+1: