The current GATK version is 3.6-0

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# Error Using RealignerTargetCreator

Hello

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:

##### ERROR contig reference = chrM / 16569.

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?

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