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

Usage: gh

Steps:

1. photo output-file
   This keeps record of this session in output-file
2. load marker locus-file
   Note that we can put cM distances instead of recombination fractions in locus file.
3. haplo off
   Since we do not want any haplotyping done. By default it is on. There are other programs to do haplotyping also.
4. use
   To check the map loaded. 'use' can be used with parameters to specify a new map.
5. single on
   If you want to do single locus analysis. By default it is off
6. scan pedigree-file
   Reads in pedigree file and does the analysis.
7. total
   Summarizes results for all pedigrees
8. quit

   Creates output file specified in step 1.