Chip-Seq Peak Caller Able To Find Peaks Split By Indels?

Are there any chip-seq peak callers able to find cases where the region under a peak has been split by an indel between the reference and the chipped sample?

For example, let's suppose one has done chip-seq on individual 1. Let's suppose we were to resequence individual 1, assemble the genome, and map the chip-seq reads straight to its assembled genome, and there would a peak like this:

         ***
        *****
      **********
    **************
 ********************
-----------------------

Now the reference genome has an insertion with respect to the chipped sample, so when one maps chip-seq reads from individual 1 to the reference genome assembly, the peak looks like this:

         *                    **
        **                    ***
      ****                    ******
    ******                    ********
 *********                    ***********
----------====================-------------

Is there any peak caller able to identify this as a single peak, even if the indel is in the range of hundreds of bps?