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gagneurlab / MMSplice_MTSplice

Tissue-specific variant effect predictions on splicing
MIT License
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Interpretation of Results #48

Closed astarr97 closed 3 years ago

astarr97 commented 3 years ago

Is there somewhere with more information on the output of MMsplice, specifically the pathogenicity and efficiency score? What do these numbers represent? What is a reasonable cutoff to say that a variant is likely to affect efficiency significantly or likely to be pathogenic? Thanks in advance.

MuhammedHasan commented 3 years ago

Dear @astarr97,

Pathogenicity and efficiency scores are probabilities so you may use a cut-off accordingly.

Moreover, the main scores is delta_logit_psi. If |delta_logit_psi| > 1, it is likely splice disturbing variant. If it is |delta_logit_psi| > 5, more likely to disturbing splicing. If it is |delta_logit_psi| < 1, a variant is not likely to disturbs splicing.

astarr97 commented 3 years ago

Great thank you!