Changes

=== Basic Output Options ===

=== Basic Output Options ===

   -b ''base call file''             Specifies the name of the output [[VCF]]-format base call file

   -b ''baseCallFile''               Specifies the name of the output [[VCF]]-format base call file

   -p ''threshold''                  The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''

   -p ''threshold''                  The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''

   --reference                    Positions called as homozygous reference will be included in the output.   

   --reference                    Positions called as homozygous reference will be included in the output.