Remove deprecated --use-new-qual-calculator.
Remove deprecated --use-new-qual-calculator.

Deprecated in GATK 4.1.5.0.

See https://github.com/broadinstitute/gatk/pull/6398.

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