Documentation for AUTOSCAN 1.0 & 1.0.1


Autoscan is a Unix computer application for automated use of linkage
analysis programs.

              Written by Tero Hiekkalinna (Juntunen)
            (C) 1999-2000 Tero Hiekkalinna (Juntunen)



			   CONTENT

		1. ABSTRACT
		2. GENERAL RERQUIREMENTS
		3. INSTALL INSTRUCTIONS
		4. WARRANTY

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1. ABSTRACT
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The use of linkage analysis programs consists of multiple file handling
processes and production of input files specific for various statistical
programs. This basically trivial process is time consuming and error 
prone since it repeats basic steps multiple times. Our aim was to develop
 helper program to automate the tedious process of the creation of input
files from genotype data of genome-wide scans, which would allow efficient
analyses of several different phenotypic traits. In practice, this program
enables the analyses of a whole genome-wide scan for all chromosomes in a
single run. 

Our Unix-shell-script program AUTOSCAN automatically creates
data files, uses MAKEPED (converts pre-linkage format files to linkage 
format), DOWNFREQ (estimates allele frequencies from pedigree data), and 
PEDCHECK (Mendelian checking) programs and finally starts statistical 
analyses via the ANALYZE package. ANALYZE performs parametric linkage 
analysis (MLINK), nonparametric affected sib-pair analysis (ASP), 
family-based association analysis (TDT, HRRR), and homogeneity testing 
(HOMOG). Input files for AUTOSCAN are the pedigree files for all chromosomes,
the disease model file, the number of loci file, and the ANALYZE input file.
The AUTOSCAN also allows easy handling of several phenotype traits and trait
features by only changing the disease model file after each run. The program
has now been tested by several research groups in the Department of Human 
Genetics, UCLA, and is available for downloading from our web page 
http://www.genetics.ucla.edu/software/autoscan 

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2. GENERAL REQUIREMENTS for AUTOSCAN 1.0.1
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1. Unix Operating System (Tested on Linux, Solaris 2.6 and Digital Unix 4.0D)
2. C-compiler (Compiling amakedata)
3. ANALYZE Package (ftp://linkage.cpmc.columbia.edu/software/analyzenew)
4. LINKAGE (FASTLINK) Package (ftp://fastlink.nih.gov/pub/fastlink) 
5. DOWNFREQ (ftp://linkage.cpmc.columbia.edu/software/analyzenew)
6. MAKEPED (ftp://linkage.rockefeller.edu/software/linkage/UNIX)
7. LSP (ftp://linkage.rockefeller.edu/software/linkage/UNIX)
8. PEDCHECK (ftp://watson.hgen.pitt.edu/pub/pedcheck)

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3. INSTALL INSTRUCTIONS
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Doanload autoscan101.tar.Z from http://www.genetics.ucla.edu/software/autoscan
and uncompress/untar it:

uncompress autoscan101.tar.Z
tar -xvf autoscan101.tar

Tar file includes:

amakedata.c	(Source code for amakedata, which makes datafiles)
autoscan10.sh	(Bourne shell script - AUTOSCAN 1.0 program)
autostart	(Bourne shell script - Program for starting autoscan10.sh)
Makefile	(Makefile for amakedata.c)
README.install	(Install instructions)
README.use	(Use instructions)
README.amakedata(Help file for amakedata)
Sample Files	(2-point and multipoint dataset)

AMAKEDATA:
==========
Compile amakedata by using "make" (Requires cc or gcc compiler, edit Makefile if
you like to use other than cc compiler.):

make

AUTOSCAN101.SH:
==============
Check line 38 that analyzeprep/analprep command is same as in your system.

If you are running AUTOSCAN under Solaris you should modify autoscan101.sh from
line 47 and put is as:

CALCWORK=/tmp/calctmp$$

Because /tmp folder in Solaris (2.6) is actually RAM so analysis are much much more 
faster then. So if your Unix system has partition which is actually RAM, use that.

EXECUTABLES:
============
Make sure that autostart and autoscan101.sh has 'executable' flag. If they don't
have, type following:

chmod a+x autostart autoscan101.sh

Copy amakedata, autoscan10.sh, autostart to you 'bin' directory, e.g. 
/usr/local/bin.

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4. WARRANTY
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THIS SOFTWARE COMES WITH ABSOLUTELY NO WARRANTY! USE AT YOUR OWN RISK!


(Doc version 1.0.1, 12/20/2000)