7.2 Sample ibddrop parameter file

Files for ibddrop may be found in the `IBD' subdirectory of `MORGAN_Examples'. The sample parameter file for ibddrop is `jv_rep_ibd.par'.

input pedigree file "jv_rep.ped" simulate markers 5 trait 1 map markers distances 44.6 44.6 11.2 11.2 map trait 1 marker 2 distances 22.3 set component 1 proband gametes 331 0 333 1 set component 2 proband gametes 541 0 541 1 341 0 343 1 input seed file '../sampler.seed' set MC iterations 20000

The parameter file specifies the pedigree file name `jv_rep.ped' and then asks for five markers and one trait locus. Since there are no data, the distinction between marker and trait doesn't mean anything -- it is just a way to specify a set of loci, one of which may be unlinked. `jv_rep.ped' contains data on 30 individuals, including gender and one trait.

The two `map' statements specify the genetic map. From the first statement, the genetic distances between the markers are 44.6, 44.6, 11.2 and 11.2 centiMorgans. From the second statement, the trait lies between markers 2 and 3, at 22.3 centiMorgans with marker 2.

The `set proband gametes' statements tell ibddrop which gametes to score: that is, the gametes among which the ibd probabilities will be estimated. In this example, we selected, from component 1 (the first family in the data set), the maternal (0) gamete of `331' and the paternal (1) gamete of `333'. The next statement selected four gametes to score from family 2. Note that characters are allowed in the names of individuals.

The `input seed file' statement enables the file to use the seeds from file `sampler.seed'. The `output overwrite seed file' statement allows the program to replace the contents of the seed file with the newly generated seeds. If this options were omitted, when the program finished running, new seeds would be appended to the end of the file. Seeds can also be set using the `set sampler seeds' statement (see ibddrop statements).

The number of Monte Carlo iterations is set to be 20,000 by the `set MC iterations' statement.

Note that if one would like to compute multilocus ibd probability, the statement `set locus window' can be used to specify number of loci to score simultaneously. ibddrop has limited functionality for computing multilocus probabilities, it can only examine two gametes to determine whether or not the two are ibd. For instructions on how to implement windows in this example, see the parameter file. For additional options, including specific patterns over two or more gametes, see Sample lm_auto parameter file.