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.)