GATK joint: use batch size to avoid memory slowdowns on large inputs
GATK joint: use batch size to avoid memory slowdowns on large inputs

Fixes #2852

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