canonical transcript from vep

Question

[romain.lannes]

I am using VEP and I wonder which transcript to report. I am aware this is an opinionated question.

Furthermore, I know VEP has a canonical transcript field, but in fact this follow the longest transcript rule as described here: How does VEP decide on canonical transcripts and is there a list?

VEP also give "appris" and "tsl" score.

Because It can often change the result, I wonder I if I can do better than "the longest rule" when possible. Does it exist a state-of-the-art method to pick the "Canonical transcript" (i.e. a supported transcript likely to be the majority one).

Answer 1

[Emily]

No, that's been updated since then. Details here.