update germline workflows to produce genome vcfs and genotyped vcf

[apaul7]

During the transition to GATK4 the method for producing a genotyped vcf was changed. With GATK4, the HaplotypeCaller tool produces the genotyped vcf. This is happens when the --emit-ref-confidence option is set to NONE.

With GATK3, the HaplotypeCaller tool produced genome vcfs(gvcfs). These gvcfs were genotyped in the next step with GenotypeGVCFs. This allowed the pipeline to produce gvcfs and a final genotyped vcf.

After discussing with Tom(#1037) I think the method used with GATK3 should be the default for the germline pipelines. Might be best to avoid merging #1037 and make a new PR adding the GenotypeGVCFs step.

steps:

• add back in the GenotypeGVCFs step
• update/add emit_reference_confidence enum input
  remove the NONE option for pipeline inputs since the GenotypeGVCFs step will be used
• add gvcf outputs
• add documentation