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Bioinformatics Advance Access published online on January 12, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti264
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Bioinformatics © Oxford University Press 2005; all rights reserved.
Received December 4, 2004
Accepted January 6, 2005

Applications note

ALOHOMORA: a tool for linkage analysis using 10K SNP array data

Franz Rüschendorf 1* and Peter Nürnberg 2

1 Bioinformatics Department, Max Delbrück Center (MDC) for Molecular Medicine, Berlin-Buch, Germany; Gene Mapping Center, Max Delbrück Center (MDC) for Molecular Medicine, Berlin-Buch, Germany
2 Gene Mapping Center, Max Delbrück Center (MDC) for Molecular Medicine, Berlin-Buch, Germany; Cologne Center for Genomics, University of Cologne, Cologne, Germany

* To whom correspondence should be addressed.
Franz Rüschendorf, E-mail: fruesch{at}mdc-berlin.de


  Abstract

Summary: ALOHOMORA is a software tool designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such like the Affymetrix GeneChip® Human Mapping 10K Array. Genotype data are converted into appropriate formats for a number of common linkage programs and subjected to standard quality control routines before linkage runs are started. ALOHOMORA is written in Perl and may be used to perform state-of-the-art linkage scans in small and large families with any genetic model. Options for using different genetic maps or ethnicity-specific allele frequencies are implemented. Graphic outputs of whole-genome multipoint LOD score values are provided for the entire data set as well as for individual families.

Availability: ALOHOMORA is available free of charge for non-commercial research institutions. For more details, see http://gmc.mdc-berlin.de/alohomora/.


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