Remove mapping quality flag for FreeBayes. This is taken into account by default in recent versions: http://bcbio.wordpress.com/2013/10/21/updated-comparison-of-variant-detection-methods-ensemble-freebayes-and-minimal-bam-preparation-pipelines/#comment-1495
Remove mapping quality flag for FreeBayes. This is taken into account by default in recent versions: http://bcbio.wordpress.com/2013/10/21/updated-comparison-of-variant-detection-methods-ensemble-freebayes-and-minimal-bam-preparation-pipelines/#comment-1495

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