  Neutrinos produced in the atmosphere traverse a column density of air before
being detected at neutrino observatories like IceCube or KM3NeT. In this work,
we extend the neutrino flavor evolution in the {nuSQuIDS} code accounting for
the varying height of neutrino production and the variable air density in the
atmosphere. These effects can lead to sizeable spectral distortions in standard
neutrino oscillations and are crucial to accurately describe some new physics
scenarios. As an example, we study a model of quasi-sterile neutrinos that
induce resonant flavor conversions at neutrino energies of ${O}(300)\text{
MeV}$ in matter densities of $1 \text{ g/cm}^3$. In atmospheric air densities,
the same resonance is then realized at neutrino energies of ${O}(300-
700)$~GeV. We find that the new resonance can deplete the $\nu_\mu +
\overline{\nu}_\mu$ flux at the IceCube Neutrino Observatory by as much as
$10\%$ in the direction of the horizon.
