Description

GENEHUNTER provides the researcher with wide range of analyses for performing linkage and disequilibrium analyses. It can very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size. This information is then used in exact computation of multipoint LOD scores, non-parametric linkage statistics, and now in a wide range of sibpair analyses (as in MAPMAKER/SIBS) and a new variance components analysis. In addition, several TDT analyses are also available for searching for association/disequlibrium in addition to linkage. Quick calculations involving dozens of markers, even in pedigrees with inbreeding and marriage loops, is possible with GENEHUNTER.

GENEHUNTER is intended to be used interactively on Helix. To run a GENEHUNTER job, log on to helix.nih.gov and type program name gh.

Version

Type gh on command line

Sample session

% gh
************************************************************************
*                                                                      *
*                GENEHUNTER - Complete Linkage Analysis                *
*                           (version 2.1_r6 )                          *
*                                                                      *
************************************************************************

Type 'help' or '?' for help.
Can't find help file - detailed help information is not available.
See installation instructions for details.

npl:1>load markers linkloci_1.dat
Parsing Linkage marker data file...
11 markers read (last one = locus11)

npl:2> scan pedigrees ./linkped_1.pre

analyzing pedigree ped1...
using non-originals:  20 21 22 23 24
position  LOD score    NPL score  p-value    information
   0.00   -3.094100    -0.816497  1.000000    0.875000
   2.00   -1.863181    -0.767048  0.437500    0.575444
   4.00   -1.417435    -0.726737  0.437500    0.426192
   [...]
 100.00    0.901053     0.816497  0.437500    0.875000


analyzing pedigree ped2...
using non-originals:  20 21 22 23 24
position  LOD score    NPL score  p-value    information
   0.00   -3.094100    -0.816497  1.000000    0.875000
   2.00   -1.863181    -0.767048  0.437500    0.575444
   4.00   -1.417435    -0.726737  0.437500    0.426192
   [...]
 100.00    1.201625     2.449490  0.062500    1.000000
npl:3> quit

        ...goodbye...

Documentation

http://linkage.rockefeller.edu/soft/gh/