4.2 Sample kin parameter file

Files for kin may be found in the `IBD' subdirectory of `MORGAN_Examples'. Below is a sample kin parameter file, `jv_rep_kin.par'.

input pedigree file 'jv_rep.ped' compute component 1 kinship coeff 531 431 431 432 compute component 1 inbreeding coeff 332 531 compute component 2 kinship coeff 341 442 compute component 2 inbreeding coeff 441 541 compute component 1 two-locus inbreed coeff 531 compute component 2 two-locus inbreed coeff 441 set recomb freqs .01 .05 .04 .10 .18 .30 .50 .0

The statements on lines 2 -- 7 request computation of kinship coefficients for the pairs `531 431' and `431 432', and then inbreeding coefficients for individuals `332' and `531', from component 1. It then requests kinship coefficients for the pair `341 442' and inbreeding coefficients for individuals `441' and `541' from component 2. Finally, it requests the two-locus inbreeding coefficient for `531' from component 1 and `441' from component 2. The two-locus inbreeding coefficient will be computed for two loci at distances specified in the `set recomb freqs' statement. (Note these need not be ordered, but the program will order them in the output.) If there is more than one component (connected pedigree) in the file, the component number must be specified. MORGAN assigns component numbers to the connected pedigrees within the pedigree file. If your data set contains more than one component, you may first run pedcheck to determine which individuals are assigned which component numbers.