This section contains a step-by-step walk-through of moving data through Genehunter 2 and QMS2
Initially the data will have to be prepared in a format suitable for Genehunter 2. You should have two files:
A file containing the marker information and distances. In this example, the file will be referred to as linkage.dat.
A file containing the genotypes and phenotypic scores for each individual in the sample. In this example, the file will be referred to as genehunter.ped.
Once these files are ready, they need to be run through Genehunter 2 to produce IBD data. The commands in my_genehunter.in will create the file dump.ibd which contains the IBD values for each pairing.
Example 3-1. my_genehunter.in
disp score off load mark linkage.dat increment distance 2 scan ped genehunter.ped dump ibd dump.ibd quit |
The commands in my_genehunter.in can either be typed directly into Genehunter 2, or can be redirected from the command line:
| Warning |
When using redirection, if dump.ibd, or whatever file is specified after dump ibd, exists, then Genehunter 2 will not save the IBDs. |
$ gh2 < my_genehunter.in |
analyzing pedigree 649... using non-originals: 3 4 5 6 analyzing pedigree 650... using non-originals: 3 4 5 6 npl:6> file to store IBD distribution [ibd_dist.out]: npl:7> ...goodbye... $ |