I have used pindel (version 0.2.4t) to look for indels in two strains that had a gene knocked out and replaced with an antibiotic resistance gene. The two mutants grew despite the knockout and we were looking for other mutations that may have led to this phenotype. Pindel didn't identify the knockout as either a deletion or an insertion, or any of the other outputs for that matter. Should it have? I have identify another deletion in another strain with pindel (not a deletion/insertion combo as in my two strains, just a regular deletion), so I'm pretty sure I'm running pindel correctly. Any thoughts?
I ran it with default settings, using wildtype as reference (fully assembled, closed genome).