GATK: Only include depth for non-exome VQSR runs
GATK: Only include depth for non-exome VQSR runs

Synchronize with GATK best practices

vladsaveliev/bcbio-nextgen,vladsaveliev/bcbio-nextgen,lbeltrame/bcbio-nextgen,a113n/bcbio-nextgen,biocyberman/bcbio-nextgen,biocyberman/bcbio-nextgen,chapmanb/bcbio-nextgen,lbeltrame/bcbio-nextgen,lbeltrame/bcbio-nextgen,biocyberman/bcbio-nextgen,a113n/bcbio-nextgen,a113n/bcbio-nextgen,vladsaveliev/bcbio-nextgen,chapmanb/bcbio-nextgen,chapmanb/bcbio-nextgen