mrkdouble

Analyzes possible equivalent haplotypes (pairs of markers whose genotyping are ``compatible'' and could therefore be merged) in the current markers selection.

Synopsis :

The mrkdouble command is invoked either as:

• mrkdouble Options
• mrkdouble

Description:

mrkdouble analyzes, for each pair of marker, if the two markers have compatible genotyping (i.e. if the genotyping of the two markers can be assumed to be the same w/o any inconsistency). When two markers are ``compatible'', their two-points LOD are presented to decide to merge (or not) the two markers (compatible markers with null LOD are simply markers that are compatible because they do not share any information and should therefore not be merged).

Arguments :

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.

Example:

# we first load a data set
CG> dsload Data/bc.cg
{1 f2 backcross 20 208 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/b...
# and select some markers in it
CG> mrkselset {11 12 13 14 15 16 17 18 19 20}

# this identifies pairs of markers that can be merged
CG> mrkdouble

Possible double markers:

               MS11 = MS14            [3.6]
               MS12 = MS13            [18.7]
               MS12 = MS14            [3.6]
               MS13 = MS14            [6.0]
               MS14 = MS16            [3.6]
               MS14 = MS17            [1.5]
               MS17 = MS18            [16.0]

See also:

• mrkmerges (2.3.10)
• mrkmerge (2.3.9)
• mrkselset (2.3.14)
• mrkmerge (2.3.7)