Running pindel in single-end mode

Question

[Gandalf]

Is it possible to run Pindel in single-end mode? In my case, Pindel program is failing because the paired-end 250 bp reads (500 bp in total) are larger than the amplicon size. I think this should not be possible since Pindel relies on paired-end reads to determine the indels but I was wondering if there is a way around it.