readme -- GIST package, version 0.3
Last update 03/24/2004


0.  The GIST package (version 0.3) contains the following files:

gist.c -- main program
CORR.h -- library containing estimated correlation coefficients
readme -- this file
sample.dat -- sample input file
sample.out -- sample output
sample.sas -- sample SAS code for calculating the three weight variables
history -- version history



1.  To extract these files from the package, type
    tar -zxf gist.tar.gz

This will generate a subdirectory GIST, which contains the files
listed above.

To compile the program in Unix/Linux, go into the GIST directory and type
    gcc -lm -o gist.exe gist.c



2.  The program can be executed by command:
    gist.exe inputfile [outputfile]

If the output file name is omitted, the standard output will be used.



3.  The format of the input file is as follows:

The first line has one number -- the frequency of the target allele.

Starting from the second line, each line corresponds to a family and
should have four numbers -- weight for dominant model, weight for
recessive model, weight for additive model, and family NPL score at
the marker locus, respectively.

A sample input file is included in this package.

A number of existing programs can output allele frequency.  The three
weight variables can be calculated using software like SAS, S-plus,
and R.  A sample SAS program is included in this package.  The family
NPL scores can be obtained from GENEHUNTER output files.



4. The method is described in

Li C, Scott LJ, Boehnke M. (2004) Assessing Whether an Allele Can Account
in Part for a Linkage Signal: The Genotype-IBD Sharing Test (GIST).
Am. J. Hum. Genet. 74:418-431

GIST is developed and maintained by Dr. Chun Li of Vanderbilt University.
Please send your comments and suggestions to chun.li@vanderbilt.edu.

The latest version of the software can be obtained from
http://biostat.mc.vanderbilt.edu/ChunLiPublic