I'm trying to merge to bam files, one mapped and another unmapped, with gatk (MergeBamAlignment) but I keep having this error all the time:
Inappropriate call if not paired read
Does anybody know why? I found this post (gatkforums.broadinstitute.org/gatk/discussion/12259/mergebamalignment-problem) where the user have the same type of problem, but changing the alignment solves it but unluckily I can't do that.
When I run
ValidateSamFile from Picard, I don't have any errors for both bam files.
Any help is appreaciate it! Thanks in advance!