We study the index of the APS boundary value problem for a strongly Callias-type operator D on a complete Riemannian manifold $M$. We show that this index is equal to an index on a simpler manifold whose boundary is a disjoint union of two complete manifolds $N_0$ and $N_1$. If the dimension of $M$ is odd we show that the latter index depends only on the restrictions $A_0$ and $A_1$ of $D$ to $N_0$ and $N_1$ and thus is an invariant of the boundary. We use this invariant to define the relative eta-invariant $eta(A_1,A_0)$. We show that even though in our situation the eta-invariants of $A_1$ and $A_0$ are not defined, the relative eta-invariant behaves as if it was the difference $eta(A_1)-eta(A_0)$.
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