Describe the issue:
DeepVariant currently outputs default as the sample name for empty VCFs (related to the fix in #186 ). Ideally, the sample_name should be transferred from the original BAM file, but if that is too difficult to implement (since there are no examples), I think it would also be ok if we let the user customize this ID. One suggestion is that it can use the value provided by the --sample_name flag (currently, used for make_examples, but I think it can also be reused for postprocess_variants).

Using default causes issues in pipelines where the VCF is used downstream of DeepVariant (e.g. merging the VCF with other callers; or even within DeepVariant in a pipeline that scatters calling across multiple chromosomes and tries to gather them and some of those VCFs are empty).

Setup

• DeepVariant version: v0.10.0
• Installation method (Docker, built from source, etc.): docker