AUTOGSCAN: powerful tools for automated genome-wide linkage and linkage disequilibrium analysis.
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.
Hiekkalinna
Tero
T
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
Terwilliger
Joseph D
JD
Sammalisto
Sampo
S
Peltonen
Leena
L
Perola
Markus
M
D008040:Genetic Linkage / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D015810:Linkage Disequilibrium; D012984:Software