GATK really does not like alphabetically sorted references. http://gatkforums.broadinstitute.org/discussion/1204/what-input-files-does-the-gatk-accept
Does it make sense to rearrange genomes to be sorted in [chr1,chr2, chr3,...] order instead of [chr1,chr10,chr11,...] order before indexing? Lots of tools care about sorting… are there any that must have alphabetical order and not numerical order? Brad -- Brad Langhorst langho...@neb.com<mailto:langho...@neb.com>
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