The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
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.