Necessary to run FixMateInformation?
I read a previous discussion http://gatkforums.broadinstitute.org/discussion/comment/23225. I am wondering if an extra FixMateInformation step needs to be added after 'IndelRealigner'? In that discussion, seemed like 'Markduplicates' was done after 'IndelRealigner'. Or maybe he performed 'Markduplicates' twice, both after bwa mapping and 'IndelRealigner'? Even the distance information was changed. It doesn't matter if you don't perform 'Markduplicates' again. Not sure if I understand correctly? So my question is in what case do you need to perfom FixMateInformation?