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GATK resource bundles scattered_calling_intervals exclude small contigs
I was just going over some Haplotypecaller and VQSR results generated using your best practices Cromwell workflows, and found that the scattered_calling_intervals files you provide (and which those workflows use to operate over) do not cover the whole genome. For hg38, chrM and all of the alt/unplaced contigs are excluded. For b37, chrY is also excluded.
This seems like a fairly major bug that would cause people running your best practices to lose a good number of potentially important variants.