T. Hiekkalinna, L. Peltonen
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.
Autoscan does not work with X or Y chromosomal data.
Latest version for Solaris and Digital Unix is 1.0.1 (02/25/2000) autoscan101.tar.gz
Latest version for Linux is 1.0.1B (12/20/2000) autoscan101-linux.tar.gz
General readme files: README.install, README.use and README.amakedata
Changes from version 1.0: Minor bug fixes. All users should update to version 1.0.1.
Tar file includes:
Autoscan is tested in Linux, Solaris 2.6, 2.8 and Digital Unix 4.0D operating systems.
Precompiled binaries and sources (ANALYZE, DOWNFREQ, MAKEDATA, etc...) can be downloaded from my site.
Precompiled LINUX binaries, download here.
Tero Hiekkalinna firstname.lastname@example.org
Updated: June 11, 2002