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Bioinformatics Advance Access published online on July 12, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti571
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received March 2, 2005
Revised June 15, 2005
Accepted July 3, 2005

Applications note

easyLINKAGE-plus - automated linkage analyses using large-scale SNP data

K. Hoffmann 1 and T. H. Lindner 2*

1 Institute of Medical Genetics, Charité, Humboldt University Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
2 Division of Nephrology, Department of Medicine, Medical University Clinic at the University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany; Department of Clinical Biochemistry and Pathobiochemistry, Medical University Clinic at the University of Würzburg, Versbacher Str. 5, 97078 Würzburg, Germany

* To whom correspondence should be addressed.
T. H. Lindner, E-mail: tom.lindner{at}mail.uni-wuerzburg.de


  Abstract

Summary: We extended the original easyLINKAGE program by enabling linkage analyses for large-scale SNP data in addition to those of microsatellites. We implemented new modules for Allegro, Merlin, SimWalk, GeneHunter Imprinting, GeneHunter TwoLocus, SuperLink, and extended FastSLink by automatic loop breaking and new outputs. We added conditional linkage analyses as well as multipoint simulation studies. We extended error test routines by checking for Mendelian/Non-Mendelian genotyping errors and for deviations from Hardy-Weinberg-Equilibrium. Data can be analyzed in sets of markers, in defined centimorgan intervals and by using different allele frequency algorithms. The outputs consist of genome-wide as well as chromosomal postscript plots of LOD scores, NPL scores, P values, and other parameters.

Availability: http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/download.htm.

Supplementary information: Supplementary information is available on the website. The current version is v4.00beta.


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