mrkmerges

Merges all pairs of compatible markers detected by mrkdouble.

Synopsis :

The mrkmerges command is invoked either as:

• mrkmerges Options
• mrkmerges

Description :

The command is used to merge all pairs of markers whose observed genotypes on all individuals are compatible with each other (closely related markers for which no recombination/breakage has been observed) and at least one individual is genotyped for the two markers (i.e. LOD 2pt between the two markers is strictly greater than 0). Notice that marker1 can be compatible with marker2 and marker3, but after merging marker1 with marker2, the resulting genotyping vector corresponding to this group of two markers may be no more compatible with the one of marker3. mrkmerges checks this case, possibly reporting that two markers are no more compatibles.

Arguments :

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.
• : without parameters, merges all pairs of compatible markers.

Returns :

Nothing

Example :

   CarthaGene version 1.2-LKH, Copyright (c) 1997-2010 (INRA).

   CarthaGene comes with ABSOLUTELY NO WARRANTY.
   CarthaGene is free software. You are welcome to redistribute it,
   under certain conditions. See the License file for information.

Type 'help' for help.

# 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 ask for markers that can be merged
CG> mrkdouble

Possible double markers:

                MS9 = MS10            [7.2]
                MS9 = MS14            [3.6]
               MS10 = MS11            [3.6]
               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]


# then merge all compatible markers
CG> mrkmerges

See also :

• mrkdouble (2.3.8)
• mrkmerge (2.3.9)