GATK: continue to filter duplicates for pre-aligned
GATK: continue to filter duplicates for pre-aligned

Avoids skipping DuplicateReadFilter for pre-aligned inputs (that
presumably have been pre-duplicated) when calling with GATK
and MuTect2. Thanks to @scatreux

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