Broman KW (2010) Genetic map construction with R/qtl. Technical report #214, Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison

Genetic map construction remains an important prerequisite for quantitative trait loci analysis in organisms for which genomic sequence is not available. Surprisingly little has been written about the construction of genetic maps, particularly regarding the many practical issues involved. We provide an overview of the process, including a description of the key facilities in the R/qtl software. The process is illustrated through simulated data on an F2 intercross derived from two inbred strains.

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