Changes

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

   -b ''base call file''              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.   

   --verbose                         Print debug information to the screen

   --verbose                     Print debug information to the screen

=== Filtering According to Depth and Map Quality ===

=== Filtering According to Depth and Map Quality ===