Version

2.1.R5, installed in HIPPU

Description

GENEHUNTER provides a wide range of analyses for performing linkage and disequilibrium analyses. The backbone of the system is the 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 a wide range of sibpair analyses (as in MAPMAKER/SIBS) and a 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. Additionally, the multipoint inheritance information allows the reconstruction of maximum-likelihood haplotypes for all individuals in the pedigree and information content mapping which measures the fraction of the total inheritance information extracted from the marker data.

GENEHUNTER can be used for:

1. parametric (LOD-scores) or non-parametric (NPL-statistics) multipoint linkage analysis

2. information content calculations (PIC-value)

3. haplotype reconstruction

4. sibpair analysis (replaces MAPMAKER/Sibs)

5. variance component analysi

6. TDT-tests

The new version (2.1) of GENEHUNTER allows analysis of larger pedigrees than before.

Usage

Program is installed in Hippu (hippu.csc.fi).

To set up GENEHUNTER type:

module load genehunter

To run GENEHUNTER type:

gh

The most important commands inside the GENEHUNTER program:

1. load xxxparfile, to load the parameter file (where xxxparfile is the name of your parameter file)

2. haplotype on, to determine the most likely haplotypes for individuals

3. scan xxxpedfile, to calculate LOD scores and NPL statistics (where xxxpedfile is the name of your pedigree file)

4. total stat, to sum the LOD and NPL scores over all families

Input files:

1. Parameter file (xxxparfile e.g. datain.dat) is a standard LINKAGE data file in MLINK-format.

2. Pedigree file (xxxpedfile e.g. pedin.pre) is a standard LINKAGE data file BEFORE running MAKEPED of the LINKAGE-package.

Documentation

GENEHUNTER has a capability to on-line help e.g. by typing help scan, you will get information about the command 'scan'.

More detailed description about how to run the programs are available in the HTML document (for version 2.0) and in the PDF documentation. (In order to be able to read a PDF file you need Acrobat Reader)

Formats for the LINKAGE files can be found from the HTML version of the manual.

References

For all of these programs cite:

L. Kruglyak, M.J. Daly, M.P. Reeve-Daly, and E.S. Lander. "Parametric and Nonparametric Linkage Analysis: A Unified Multipoint Approach". American Journal of Human Genetics 58:1347-1363 (1996).

L. Kruglyak and E.S. Lander. "Faster Multipoint Linkage Analysis Using Fourier Transforms". Journal of Computational Biology 5:1-7 (1998).

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