I realise I don't have a good definition for the vertical tangent bundle in the case of a Lefschetz fibration $(E,F)\to (S,\partial S)$ ($F$ is the subbundle given by the tangent bundle of the Lagrangian boundary condition over $\partial S$.
usually the vertical sub bundle is defined as the kernel of the differential of the projection map, and that is a bundle if the rank of such map is locally constant, but the entire point of Lefschetz fibrations is that $\pi$ has critical points, so the set of kernels in each fiber do not amount to a bundle.
Nonetheless we have concepts like the relative Chern class for that "bundle", as in P. Seidel's - Fukaya Categories and Picard-Lefschetz Theory. After Lemma 17.5 he computes the index of the linearised Cauchy-Riemann operator for J-hol sections as some integral of the relative Chern class pulled back via the section $u$.
I feel this might be a stupid question but I cannot find an answer in the classical literature and I'm quite puzzled.