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Old 06-27-2011, 07:20 AM   #1
Location: Baltimore MD

Join Date: Jun 2011
Posts: 18
Question GATK RealignerTargetCreator Error = Contigs do not match

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!
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