I'm a relative newbie to Pindel, and I have some questions about the output. I'm looking at my results, specifically the file with the
_D extension. At some point in the file, it looks like the variants transition from deletions to insertions, ie there are gaps in the reads from my samples (deletions) and then all of a sudden there are gaps in the reference sequence (which I read as an insertion). My understanding was that the insertions should be in the
_SI file if they're small. Am I misinterpreting things? I prepared a screen shot to show how the transition in the file looks, but I can't seem to figure out how to attach an image here. Any help would be much appreciated.