Avoid incorrect alt alleles from bcftools view -a
Avoid incorrect alt alleles from bcftools view -a

In complicated cases from FreeBayes with large numbers of duplicate
alleles, bcftools can fail and produce an empty alternative allele
(and incorrect genotype), resulting in errors downstream. This
strips off those problem cases.

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