insertion in pindel _D file?

Question

[steven_friedenberg]

Hi there,

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.

Thanks!

Steve

[mohesan]

I have noticed the same issue. Here is an image of part of a _D file. the Deletion event are separated by a row of '#'. as you can see the first event is a deletion while the second is an insertion. but both of them are outputted to the deletion event file by pindel. I've tried running pindel multiple times and I get the same results.

Answer 1

[mohesan]

It turns out that they are complex events. If you used pindel2vcf to convert the pindel outputs to vcf you will be able to see both the reference and alternative alleles for that event.