Tools like HaplotypeCaller look at a BAM file and locate places where it differs from the reference. Thats great for variant discovery, but not so great if you want to genotype a sample, because distinguish between being homozygous reference and not having sufficient data to call a variant. That is, its not safe to assume a sample is homozygous reference just because HaplotypeCaller doesn't call a SNP.

Is there an obvious way to provide a redetermined set of locations (say dbSNP) and return, say, the properly quality adjusted log-likelihood of each genotype at each location?