Cconverts the tabular pileup output from samtools mpileup to a VCF file.  
Filters on read coverage, base quality and the frequency of a variant.  
The VCF info is populated with a SAF tag that give the specific frequency (0 - 1) of a variant being observed.
This is used for filtering in the mmuff ( Missense Mutation and Frameshift Finder) workflow.