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when using scatter with CombineGVCFs walkers I get the following error: "You have asked for an interval that cuts in the middle of one or more gVCF blocks. Please note that this will cause you to lose records that don't end within your interval"
CombineGVCFs need to see all the data at once? Or at least all the chromosome at once? If it need it, I think the automatic scatter-gather for this class in scala script is working by 'LOCI' instead of 'CONTIG'.