GENEHUNTER example - Handout from 10/18/2000 course
The following is a file prepared by Richa Agarwala describing a
simple use of GENEHUNTER on a real data set. I have removed references
to the data set to avoid revealing any research information.
This describes a very simple usage. Other usages are possible.
The basic GENEHUNTER interface is a shell on top of the UNIX shell
to which you specify commands that GENEHUNTER understands.
The name of the program is formally gh, not GENEHUNTER.
Required input files:
- locusXYZ: LINKAGE/FASTLINK format locus file for loci X, Y, Z
- prepedXYZ: pre Makeped format pedigree file with markers X, Y, Z
Desired output files
- XYZ.out: multilocus output file analyzing XYZ
- single.out: output for single locus analyses of all loci
- photo output-file
This keeps record of this session in output-file
- load marker locus-file
Note that we can put cM distances instead of recombination fractions
in locus file.
- haplo off
Since we do not want any haplotyping done. By default it is on.
There are other programs to do haplotyping also.
To check the map loaded. 'use' can be used with parameters to specify
a new map.
- single on
If you want to do single locus analysis. By default it is off
- scan pedigree-file
Reads in pedigree file and does the analysis.
Summarizes results for all pedigrees
Creates output file specified in step 1.