RNA-seq variant calling: split GATK by chromosome
RNA-seq variant calling: split GATK by chromosome

Try to avoid issues on longer running samples with spark HaplotypeCaller
by splitting jobs into more manageable chunks. This is a pre-cursor to
potentially better calling and parallization with CWL. #2390

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