GATK: avoid use of HaplotypeCalllerSpark
GATK: avoid use of HaplotypeCalllerSpark

Outstanding issues like broadinstitute/gatk#4821 with HaplotypeCallerSpark
are making it difficult to get consistent large scale gVCF runs. Fall back
to multi-core parallelization and revisit Spark calling when these issues
get closed.

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