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6.2 Sample ibddrop parameter file

There are two sample parameter files for ibddrop; let's take a look at `parIBD_LL' first.

 
input pedigree file "ped45"

simulate markers 5  traits 1

map          markers   recomb fracts .2952 .2952 .1 .1
map trait 1  marker 2  recomb fract  .18

set component 1  proband gametes 331 0 333 1
set component 2  proband gametes 5v1 0 5v1 1 3v1 0 3v3 1

set sampler seeds  0x8a226a51 0xd2978c71

set MC iterations 20000

The parameter file specifies the pedigree file name `ped45' and then asks for five markers and one trait locus. Since there is 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.

These `map' statements give the genetic map. The recombination fractions between the markers are 0.2952, 0.2952, 0.1, and 0.1. The trait is between marker 2 and 3 with recombination fraction 0.18 with marker 2. Note that two recombination frequencies of 0.1 make one of 0.18, and two of 0.18 make 1 of 0.2952. (Or in cM, we have 11.15, 22.3 and 44.6 cM using a Haldane map function.)

The `set proband gametes' statements specify which gametes to score. Here we selected, from pedigree (component) 1, the maternal gamete of `331' and the paternal gamete of `333'. The next statement selected four gametes to score from pedigree 2. Note that characters are allowed in the names of individuals.

The `set sampler seeds' statement sets the seeds. Seed statements also can be given in a separate "seed" file, which is easier to update (by appending the new seeds at the end of the Monte Carlo).

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

The other parameter file, `parIBD_WU', is quite similar.

 
input pedigree file "ped45"

simulate markers 5
simulate unlinked trait 1

map markers recomb fracts .18 .18 .1 .1

set locus window 3

set component 2  proband gametes 5v1 0 5v1 1

set sampler seeds  0x8a226a51 0xd2978c71

set MC iterations 20000

Now the trait becomes unlinked and a window of size 3 is specified in the `set locus window' statement. As a result, instead of scoring the gamete at each locus separately, ibddrop scores the sliding haplotype of 3 loci (there are four of them).

Running the examples and checking the outputs will make it clearer.


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