PURPLE: use AMBER for generating allele frequencies
PURPLE: use AMBER for generating allele frequencies

Replaces GATK4 approaches with PURPLE native support, including workaround
for issues with tiny test sets.

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