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FastaAlternateReferenceMaker output contig names?
Is there any way to make the output from FastaAlternateReferenceMaker not rename the contigs?
I'm running a pipeline that (theoretically) has worked with previous verions of GATK ( https://github.com/justin-lack/Drosophila-Genome-Nexus) but is now broken because FastaAlternateReferenceMaker renames contigs.
I can fix with a one-liner but wondered if there was a native GATK option?