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Questions about the GATK hg38 resource bundle reference
I am using the GATK hg38 resource bundle reference in my workflow and I was curious if there is any documentation or literature on how the contigs were chosen. Specifically, were did all the decoy contigs come from? A second part to my question is how decoy contigs are managed in a variant calling workflow. Are they ignored by Mutect2 or do you have to filter them out?