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. 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.
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.
Input files are:
Detail information of input files can be found from Autoscan web site http://www.helsinki.fi/~tsjuntun/autoscan/ and see README.use.
Autoscan command is:
autostart
Hiekkalinna T, Peltonen L. New program: AUTOSCAN 1.0 automated use of linkage analysis programs. American Journal of Human Genetics, VOL. 65 NO. 4 Supp, (1999).