I am running pindel on some nextgen data for exploring ins, del, rpl, tandem:dup, etc. I have two questions:
I can see most of the deletions from pindel produced by the same bam files in IGV. However, I do not see most of the insertions and replacements. Can you please tell me why is that so? Are they false positive produced by pindel? Or, does IGV has a different way of predicting ins/dels/rpls than pindel? I am using all default parameters.
I know AD = "Allele depth, how many reads support this allele". Can I filter out SVs based upon AD? I found a real deletion (confirmed by sanger sequencing) predicted by pindel with AD = 8! Whereas, there are some deletions which have far more reads but turned out to be false positives. Why is that so? What happens if pindel shows AD = 0. Does that mean that the prediction is unreliable as there are no reads to support that prediction?
Sorry for so many questions. But I am banging my head for weeks to look for answers over different forums and couldn't get hold of it.
Thanks in advance.