"Contig index is Bad" Error, where does this come from?

Hi,

I'm running an analysis of some data from Complete Genomics. I've successfully converted the output to bam files and indexed them.
However when I run BaseRecalibrator and Print Reads I get this error:

Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The contig index 17 is bad, doesn't equal the contig index 18 of the contig from a string chr18

  • I should point out that the CG -> bam conversion produces separate bams for each chromosome and I'm getting the equivalent error for every file.

I've recreated the .dict and index for the reference and I've tried sorting (using Picard ReorderSam) and re-indexing the files (using samtools index) to agree with the reference. However I am still getting these errors.

Searches of the GATK community and the web, have not produced any successful suggestions, I wondered if you had any thoughts about how this error is occurring and any suggestions how I might remedy it?

BTW, I'm using GATK 2.7-4 in Java 1.7.0_25 under Mac OSX 10.7.5, which I think is fully up to date.

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