  We show that Josephson vortices in a quasi-1D atomic Bose Josephson junction
can be controllably manipulated by imposing a difference of chemical potentials
on the atomic BEC waveguides forming the junction. This effect, which has its
origin in the Berry phase structure of a vortex, turns out to be very robust in
the whole range of the parameters where such vortices can exist. We also
propose that a Josephson vortex can be created by the phase imprinting
technique and can be identified by a specific tangential feature in the
interference picture produced by expanding clouds released from the waveguides.

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