6.3 Sample markerdrop parameter file -- conditional on inheritance pattern

The sample parameter file, `ped73_mdrop_inhe.par', requests simulation of marker data conditional on an inheritance pattern. The relevant section of the file is:

map trait 3 marker 4 recomb frac 0.01 simulate markers 10 using inheritance map marker positions 10 20 30 40 50 60 70 80 90 100 set markers 1 freqs 0.13 0.66 0.16 0.05 set markers 2 freqs 0.06 0.23 0.41 0.25 0.05 . . . set markers 10 data 101 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 102 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 201 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 202 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2010 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 301 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 302 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 304 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 . . .

Again, the first three lines of each of the parameter files above are required for markerdrop. The `map trait' statement identifies the trait locus to be used in the simulation and gives its position relative to the markers on which we wish to simulate data. In this example, the trait locus follows marker 4 with a recombination fraction of 0.01. The `simulate' statement states the number of markers to be simulated and specifies simulation using the inheritance pattern. The `map marker positions' statement specifies the spacing of the markers to be simulated. Lines 4 and 5 specify allele frequencies at the first two of the ten markers. Statement `set markers 10 data' and lines below specify the missing data pattern with 0 for missing and 1 for observed.

File `ped73_mdrop_inhe.par' uses pedigree file `ped73_mdrop_inhe.ped'. The file format section and first few lines of the pedigree data setion of this file are below.

input pedigree size 73 input pedigree record names 3 integers 4 input pedigree record trait 3 integer pairs 3 4 *************************************************** 101 0 0 1 0 -1 -1 102 0 0 2 0 -1 -1 201 101 102 1 0 0 1 202 101 102 2 0 1 1

The first three columns are indices of individuals and their parents. The next two are sex and observation status. The last two columns are inheritance indicators with the first being the paternal ones and the second the maternal ones. A founder's inheritance indicators are `-1 -1'.

markerdrop can simulate data for markers linked to only one trait locus, as specified in the `map' statement in the parameter file.