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Using intervals in Mutect2

jejacobs23jejacobs23 Portland, ORMember

I would like to spread a Mutect2 run out over several intervals in order to speed it up. I am using the GATK hg38 resource bundle reference. Do I need to put in a separate interval for each contig or will listing "chr2" (for example) also include all the alternate contigs that map to chromosome 2?

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