samtools: fix ambiguous characters in VCF
samtools: fix ambiguous characters in VCF

Thanks to Moiz Bootwalla
https://groups.google.com/d/msg/biovalidation/cSEkbxDhMcM/cPf9uoR1AQAJ

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