Changes

  --minmapquality  ''reads with with mapquality falling below this threshold will be excluded''

  --minmapquality  ''reads with with mapquality falling below this threshold will be excluded''

  --genocount      ''the maximum number of genotypes compared''  

  --genocount      ''the maximum number of genotypes compared''  

  --verbose        ''generate detailed''  

  --verbose        ''print out detailed information for each hapmap position compared''

  --coverage  

  --coverage       ''print out the proportion of markers in the map file covered by at least one read''

  --countbysite    ''generate detailed statistic for each base compared''

  --countbysite    ''print out detailed mismatch counts for each base compared''

=== Other Options ===

=== Other Options ===