pipeline failed on BGZFs without variants

[allieychen]

There are BGZFs that only contain headers but no variants. The pipeline will fail for such inputs.

[mbookman]

Thanks Allie!

For context, the GATK joint genotyping workflow shards genotyping by genomic regions. Some regions may have no variants called in your cohort and so the output contains some VCFs that have 0 variants.