Using Dindel for realignment - error with duplicate reads stage 3

[morgane51]

Dear all,

I would like to use Dindel for realigning my bam files around indels.
First general question: it seems that not so many people use it, why? Is it because of the GATK IndelRealigner tool?

Nevermind, I wanted to try Dindel anyway.
But the process stops at the stage 3 (realignment in each window), because it complains about duplicate reads. The problem is that I do want to keep duplicates because I measure expression and cannot say wether duplicate reads are due to overexpressed genes or PCR biais.

Here is the message I get:
error_duplicate_reads! 38 NA Mito_Scaffold_003 6188 6308 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

I understand that it may not realign at this locus, but can't it just go forward?

I also take any suggestion for other realigner.

Thank you for you help.

Morgane