linkage user's guide (version 5.2)

3.6 CMAP

Purpose

The program CMAP performs the same function as LINKMAP but only in three-generation pedigrees with codominant marker loci.

Using the Program

CMAP functions with the program CFACTOR. The calling order is: 

     CFACTOR
     CMAP
The input files for this suite of programs are: 
     PEDFILE
     DATAFILE
The output files are: 
     OUTFILE
     STREAM
TEMPPED and TEMPDAT are temporary files produced by CFACTOR for input to CMAP.

Program Constants Specific to CMAP

See LINKMAP (section 3.4 ).

Datafile Structure

Except for the program code, which is 2 for CMAP, DATAFILE has the LINKMAP format.

Program Options

When the constant BYFAMILY is "true," likelihoods are given for each family in OUTFILE.

Comments: Recoding is used to reduce the number of alleles at each locus; see the comments in section 3.5.

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