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AUTOGSCAN: Powerful Tools for Automated Genome-Wide Linkage and Linkage Disequilibrium Analysis

  • Tero Hiekkalinna (a1), Joseph D. Terwilliger (a2), Sampo Sammalisto (a3), Leena Peltonen (a4) and Markus Perola (a5)...

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.

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Copyright

Corresponding author

*Address for correspondence: Leena Peltonen, MD, PhD, Academy Professor, National Public Health Institute, Department of Molecular Medicine, PO Box 104, 00251 Helsinki, Finland.

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AUTOGSCAN: Powerful Tools for Automated Genome-Wide Linkage and Linkage Disequilibrium Analysis

  • Tero Hiekkalinna (a1), Joseph D. Terwilliger (a2), Sampo Sammalisto (a3), Leena Peltonen (a4) and Markus Perola (a5)...

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