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 a 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.