understanding genotyping output modes

[annie...@gmail.com]

I want to genotype some bisulfite converted DNA. At this point I already have the methylation data so all I really need are the variant calls. I used the output mode EMIT_VARIANTS_ONLY. However, I only got output if is was different than the homozygous reference. I also want to know if a SNP is homozgous reference. My coverage is spotty because this is targeted so I don't want to assume that no call means homozygous reference. Can you please explain to me which option to use so that I get 0/0, 0/1, and 1/1 calls for my VCF file?

Annie