When GATK emits all sites, homref sites get the RQC annotation instead
of the QC annotations. For vtools, these two annotations are used
interchangeably, since they both contain genotype likelihoods.

See the detailed explantation at
https://gatkforums.broadinstitute.org/gatk/discussion/5115/haplotypecaller-genotypegvcfs-and-vqsr-for-alternatives-in-dbsnp