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).