7.2 Sample ibddrop parameter file

Files for ibddrop may be found in the `IBD' subdirectory of `MORGAN_Examples'. There are two sample parameter files for ibddrop; let's take a look at `jv_rep_ibd.par' first.

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. Here 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'. When the program finishes running, new seeds will be generated and appended at the end of this 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, statement `set locus window' can be used to specify number of loci to score simultaneously.