Is there a tool already out there that can add the QualityOfDepth(QD) annotation to a VCF file created by freebayes?

The general idea of variant QualityByDepth(QD) is explained here and the detailed formula is the best answer (highlighted in green) here.

Freebayes outputs somewhat different fields than GATK. Instead of AC (allele count) per genotype:

##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">

The basic QD formula should be something like.

QD = QUAL / Sum (Sum (RO+AO)) (over just the samples that have a read that contributes to the variant call).