Example of usage:
crimap 7a prepare
Prepare first searches for the
.gen and
.dat files of the correct
name (in the above example, chr7a.gen and chr7a.dat). If there
is no
.dat
file, one is created from the
.gen file; if both
exist, the program asks whether a new
.dat file should be created
from the
.gen file (select this option if the
.gen file is more
recent). If neither exists, a message to that effect is given
and the program terminates. As the
.dat file is being created,
family IDs are displayed and any non-inheritances are noted.
(These should be checked carefully: a missing data item in the
.gen file will
generally result in multiple non-inheritances and
incorrect family IDs for the subsequent families. If noninheritances
are found, these should be corrected in the
.gen
file, and prepare run again).
Prepare then displays values for several parameter values, including whether to compute sexaveraged or sex-specific likelihoods, and tolerances which control convergence of the maximum likelihood search and the map building process (see description of .par file, above). The displayed values are the defaults (given in the description of the .par file) or the values specified in any preexisting .par file of the same name. The user is then prompted to change any of these values, if desired. Any haplotyped systems, or fixed distances (see description of .par file) in a preexisting .par file are then displayed, and you are prompted to enter any new ones if desired. (prepare cannot be used to modify or delete systems in the preexisting file; you must use a text editor for this).
Prepare then displays the names of the other CRI-MAP options, and asks which one it should set up the .par file for. Depending on the option chosen, the user is now prompted to specify the indices of the "ordered loci", and of the "inserted loci". The ordered loci are generally fixed in that order during subsequent analysis, while the inserted loci are tried in all possible positions. When nothing is to be assumed about locus order only two ordered loci should be specified. (Twopoint is a special case; see its description below). For the map-building options ( build, instant, and quick ), the ordered loci form the initial map. As the default (in this case only), if requested, prepare will sort the loci by informativeness of the phase known data and designate the two most informative loci as the ordered loci, and the remaining loci as inserted.
For the options fixed, flipsn, and chrompic, all loci are specified as ordered, and none are inserted. See the description of the .par file, or the relevant option, for further details. If the option build has been specified, prepare initializes an orders file, unless one already exists, in which case it asks whether the existing one should be used.
Finally, prepare asks whether to create a new .par file containing the information you have input. You have the option at this point of aborting the creation of a new file, in which case any preexisting .par file will remain intact.
previous section: 5.7 merge
next section: 5.9 quick