GATK RealignerTargetCreator Error = Contigs do not match

[Hkins552]

I'm trying to do a local realignment using GATK and seem to be stuck at the first step. I've created my ref.dict file and then tried the following script:

$ java -jar gatk -T RealignerTargetCreator -I input.bam -R genome.fasta -o output.intervals

An error was generated which said the contigs in my reference fasta and input bam do not match. Ex: Chrom 1 vs. 1

I attempted to use Picardtools ReorderSam command to at least order them correctly, but it will not recognize that "1" in the input.bam represents "chrom 1" in the reference. Is there a way to rename the contigs on one of these files such that ReorderSam can be used?

Thanks for your input!

[Hkins552]

Contigs Do Not Match

Still running into the same error. Any input would be greatly appreciated In the mean time, I will likely write a script to rename the contigs in the file and see if that pans out.