Edit Distance Algorithm (variant of longest common sub-sequence)
the additional cost of adding a swap function should be: 

T(j-2,k-2) + Cs  , if A[j-1]=B[k],and A[j]=B[k-1]

I found the answer by studying the Damerau–Levenshtein distance modification of the classic edit distance problem.

Source: https://en.wikipedia.org/wiki/Damerau%E2%80%93Levenshtein_distance