I am currently trying to run the RealignerTargetCreator on some bam files which were aligned to hg19 howver am getting this error `ERROR MESSAGE: Input files known and reference have incompatible contigs: Found contigs with the same name but different lengths:
After some initial investigation I found that the supplied hg19 reference genome which was being used for mapping was using rCRS mtDNA. other then realigning to a different build of hg19 is there any way to easily fix this problem through GATK?
I'm trying to run some tests and can't because I get this message that my reference is not the same as the input file, even though I've been assured that it is. Is there a way around this? I'm new to this, so step-by-step details would be appreciated, thanks