title: AUTOGSCAN: powerful tools for automated genome-wide linkage and linkage disequilibrium analysis.
abstract: Genome-wide linkage analysis using multiple traits and statistical software packages is a tedious process which requires a significant amount of manual file manipulation. Different linkage analysis programs require different input file formats, making the task of analyzing data with multiple methods even more time-consuming. We have developed a software tool, AUTOGSCAN, that automates file formatting, the running of statistical analyses, and the summarizing of resulting statistics for whole genome scans with a push of a button, using several independent, and often idiosyncratic, statistical software packages such as MERLIN, SOLAR and GENEHUNTER. We also describe a program, ANALYZE, designed to run qualitative linkage analysis with several different statistical strategies and programs to efficiently screen for linkage and linkage disequilibrium for a given discrete trait. The ANALYZE program can also be used by AUTOGSCAN in a genome-wide sense.
authors.affiliation: Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
authors.forename: Tero
authors.initials: T
authors.lastname: Hiekkalinna
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Terwilliger
authors.forename: Sampo
authors.initials: S
authors.lastname: Sammalisto
authors.forename: Leena
authors.initials: L
authors.lastname: Peltonen
authors.forename: Markus
authors.initials: M
authors.lastname: Perola
mesh_terms: D008040:Genetic Linkage / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D015810:Linkage Disequilibrium; D012984:Software