7.3 Running ibddrop example and sample output

The syntax for running this MORGAN program is:

<./program> <parameter file> [ > <output file name> ]

where , optionally, `>' redirects the standard output (<stdout>) to an output file instead of to the screen.

The `ibddrop' example can be run under the subdirectory `IBD/' with the following command:

./ibddrop jv_rep_ibd.par > ibddrop.out

The genetic map specified by the statements `map markers distances' and `map trait 1 marker 2 distances' is below. Note the position of the trait locus (T1) with respect to the marker loci.

Distances (cM): T1 --------------+--------------------- 44.6 22.3 22.3 11.2 11.2 +------+-------------+------+------+ M1 M2 M3 M4 M5

Since the parameter file contains two `set proband gametes' statements, ibddrop will produce two sets of results in the output file (here `ibddrop.out').

The exact probability estimates will, of course, depend on the random seed used. Some example results for the second component are detailed below.

Summary for component 2: Probabilities of IBD patterns Proband gamete set 1: 541 0 541 1 341 0 343 1 pattern marker-1 marker-2 trait-1 marker-3 marker-4 marker-5 label 1 1 1 1 .0322 .0312 .0289 .0301 .0294 .0306 0 1 1 1 2 .0291 .0294 .0295 .0284 .0299 .0295 1 1 1 2 1 .0129 .0143 .0147 .0140 .0142 .0134 3 1 1 2 2 .0103 .0098 .0097 .0097 .0089 .0092 4 1 1 2 3 .0273 .0280 .0263 .0269 .0276 .0267 5 1 2 1 1 .0654 .0638 .0634 .0652 .0633 .0649 6 1 2 1 2 .0060 .0063 .0057 .0062 .0062 .0058 7 1 2 1 3 .0571 .0576 .0581 .0601 .0602 .0584 8 1 2 2 1 .0692 .0680 .0661 .0685 .0703 .0728 9 1 2 2 2 .0483 .0527 .0488 .0493 .0486 .0485 10 1 2 2 3 .1389 .1405 .1386 .1384 .1371 .1326 11 1 2 3 1 .1348 .1366 .1354 .1379 .1369 .1391 12 1 2 3 2 .0267 .0250 .0259 .0266 .0267 .0285 13 1 2 3 3 .0949 .0945 .0980 .0949 .0968 .0975 14 1 2 3 4 .2469 .2424 .2508 .2437 .2442 .2427 15

The probabilities are summarized by the ibd pattern. Each integer in the pattern represents one of the gametes that ibddrop was asked to score. Same numbers indicate gametes that are ibd. For instance, `1 1 1 1' means all four gametes are ibd; `1 2 1 1' means gametes 1, 3, and 4 are ibd, while gamete 2 is not ibd with the others; `1 2 3 4' means all four gametes are not ibd.

The ibd patterns are scored for each locus separately; there is a column for each of the five markers and one for the trait.

To compute multilocus ibd probabilities, say for 3 loci, follow the instructions to use `set locus window 3' in the parameter file and re-run the example using the same command line. The interesting part of the output is:

Summary for component 2: Probabilities of IBD patterns for windows of 3 loci Proband gamete set 1: 541 0 541 1 IBD wndw 1 wndw 2 wndw 3 wndw 4 0 0 0 .7291 .7443 .7657 .7881 0 0 1 .0698 .0655 .0482 .0478 0 1 0 .0640 .0532 .0365 .0266 0 1 1 .0279 .0252 .0369 .0284 1 0 0 .0806 .0696 .0703 .0493 1 0 1 .0087 .0080 .0067 .0049 1 1 0 .0135 .0238 .0177 .0268 1 1 1 .0063 .0105 .0180 .0281

This time, ibddrop was asked to compute ibd probabilities in windows of three loci at a time. This was done using the `set locus window' statement. Since the trait locus is unlinked to the marker loci in this example, it is placed to the left of the five marker loci on the map. Thus the first window, `wndw 1' in the table above, includes the trait locus and the first two marker loci, `wndw 2' includes the first three marker loci, `wndw 3' includes marker loci 2, 3 and 4, etc. The values in the `ibd' column at the left of the table represent `ibd' patterns. The pattern `0 0 0' means that the selected gametes are not ibd at the three loci in each window. The pattern `0 0 1' means that the selected gametes are not ibd at the first two loci in the window, but are ibd at the third. The values in the columns give the probability of the ibd pattern at the left for each of the four windows. For example, the probability that the maternal and paternal gametes of individual 541 are ibd at marker loci 3 and 5, but not at marker locus 4 is 0.0049.

Note that there are two additional example parameter files in the `IBD/' subdirectory; these examples are not discussed in the tutorial but are there for the interested user.