Set min_allele_fraction default by each caller
Set min_allele_fraction default by each caller

Do not default min_allele_fraction globally so we can skip it in MuTect
if not set. Default in MuTect is equivalent 2% instead of default 10%.
Switching to 2% globally is not a great choice because VarDictJava
slows down at these levels.
Based on validation work: http://imgur.com/a/3VPbq

lpantano/bcbio-nextgen,elkingtonmcb/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,fw1121/bcbio-nextgen,lbeltrame/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,gifford-lab/bcbio-nextgen,biocyberman/bcbio-nextgen,gifford-lab/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,brainstorm/bcbio-nextgen,lpantano/bcbio-nextgen,lpantano/bcbio-nextgen,lbeltrame/bcbio-nextgen,lbeltrame/bcbio-nextgen,hjanime/bcbio-nextgen,biocyberman/bcbio-nextgen,fw1121/bcbio-nextgen,a113n/bcbio-nextgen,a113n/bcbio-nextgen,verdurin/bcbio-nextgen,verdurin/bcbio-nextgen,a113n/bcbio-nextgen,chapmanb/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,gifford-lab/bcbio-nextgen,vladsaveliev/bcbio-nextgen,vladsaveliev/bcbio-nextgen,hjanime/bcbio-nextgen,brainstorm/bcbio-nextgen,mjafin/bcbio-nextgen,elkingtonmcb/bcbio-nextgen,mjafin/bcbio-nextgen,chapmanb/bcbio-nextgen,chapmanb/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,fw1121/bcbio-nextgen,mjafin/bcbio-nextgen,elkingtonmcb/bcbio-nextgen,biocyberman/bcbio-nextgen,brainstorm/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,vladsaveliev/bcbio-nextgen,hjanime/bcbio-nextgen,verdurin/bcbio-nextgen