  To every 3-manifold M one can associate a two-dimensional N=(2,2)
supersymmetric field theory by compactifying five-dimensional N=2
super-Yang-Mills theory on M. This system naturally appears in the study of
half-BPS surface operators in four-dimensional N=2 gauge theories on one hand,
and in the geometric approach to knot homologies, on the other. We study the
relation between vortex counting in such two-dimensional N=(2,2) supersymmetric
field theories and the refined BPS invariants of the dual geometries. In
certain cases, this counting can be also mapped to the computation of
degenerate conformal blocks in two-dimensional CFT's. Degenerate limits of
vertex operators in CFT receive a simple interpretation via geometric
transitions in BPS counting.
