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Intervals that cross chromosomes

jphekmanjphekman Broad InstituteMember

Hi team. I'm trying to put together an interval list (in any format that can be used by GenotypeGVCFs) that crosses chromosomes (multiple chromosomes within one interval).

This is for most efficient processing on Terra - @jsoto assures me that about 900 intervals will be ideal for processing canine samples, and our references has 3k or so contigs. I'd like to be able to combine all our tiny unanchored segments into larger intervals.

I can't find the syntax to specify an interval that includes multiple chromosomes - is it even possible? Help!

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