Hey I am working with the tool Pindel to analyse bwa sequenced reads for insertions and deletions. and I realized that some of the reported deletion events look as if they should be an insertion. Pindel returns the events it finds by first outputting the line reference genome and the the aligned reads following it. For deletion events the reference line would output the bases in lower-case if it was deleted. For insertion events it would leave a gab between the bases on the reference where the insertion occurred. In the file which was returned by pindel and is supposed to contain only deletion events, there are a few events that look like an insertion.
I want to know how I can fix this issue.
In addition some deletion events remove the bases from the reference line and replace them with <x> where x represents the number of bases removed. For example instead of AGcgtaatgctaT it would have AGcg<7>aT. I'd like to stop pindel from doing this. Any help will be much appreciated. Thank you!