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ibddrop
output Run the first example with the command:
ibddrop parIBD_LL |
The genetic map is given, semi-graphically, in the following manner,
Distances (cM): T1 --------------+--------------------- 44.6 22.3 22.3 11.2 11.2 +------+-------------+------+------+ M1 M2 M3 M4 M5 |
Check the parameter file to verify that this is indeed what we wanted. Since we had two `set proband gametes' statements, we have two sets of results. Let's take a closer look at the second one,
Summary for component 2: Probabilities of IBD patterns (pedigree based) Proband gamete set 1: 5v1 0 5v1 1 3v1 0 3v3 1 pattern marker-1 marker-2 trait-1 marker-3 marker-4 marker-5 label 1 1 1 1 .0315 .0306 .0314 .0300 .0273 .0284 0 1 1 1 2 .0295 .0294 .0284 .0295 .0317 .0307 1 1 1 2 1 .0131 .0126 .0149 .0127 .0129 .0123 3 1 1 2 2 .0097 .0106 .0100 .0097 .0089 .0092 4 1 1 2 3 .0255 .0286 .0263 .0276 .0279 .0283 5 1 2 1 1 .0638 .0635 .0658 .0644 .0645 .0650 6 1 2 1 2 .0056 .0059 .0056 .0056 .0069 .0066 7 1 2 1 3 .0581 .0595 .0589 .0609 .0593 .0590 8 1 2 2 1 .0683 .0720 .0648 .0683 .0703 .0682 9 1 2 2 2 .0520 .0488 .0494 .0490 .0491 .0487 10 1 2 2 3 .1370 .1351 .1366 .1359 .1349 .1355 11 1 2 3 1 .1369 .1303 .1366 .1316 .1348 .1379 12 1 2 3 2 .0275 .0265 .0296 .0265 .0266 .0269 13 1 2 3 3 .0965 .1013 .0961 .0997 .0974 .1009 14 1 2 3 4 .2449 .2454 .2455 .2488 .2473 .2425 15 |
The probabilities are summarized by ibd "pattern". A pattern is a series of integers with the same length as the number of gametes 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.
The second example can be run as:
ibddrop parIBD_WU |
And the interesting part of the output is
Summary for component 2: Probabilities of ibd patterns Proband gamete set 1: 5v1 0 5v1 1 ibd wndw 1 wndw 2 wndw 3 wndw 4 0 0 0 .7231 .7447 .7659 .7874 0 0 1 .0668 .0686 .0464 .0475 0 1 0 .0670 .0519 .0360 .0266 0 1 1 .0321 .0230 .0409 .0265 1 0 0 .0901 .0675 .0691 .0472 1 0 1 .0081 .0083 .0067 .0050 1 1 0 .0088 .0239 .0162 .0281 1 1 1 .0040 .0121 .0190 .0318 |
The ibd pattern is given as a series of zeros and ones with the same length as the number of loci in the window (the window size). `1' means that all gametes are ibd at that locus and `0' means, well, take a wild guess!
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