L Wu.  Locus-specific genetic effect estimates are subject to upward bias in linkage analysis if the same original dataset is used for both hypothesis testing and effect-size estimation (Göring et al. 2001). Sun and Bull (2005) proposed three bootstrap estimators to effectively remove the upward bias for a single locus model. Wu, Sun and Bull (2006) extended the bootstrap estimators to handle multiple loci and evaluated their performances in the context of estimation of locus-specific heritability in quantitative trait loci (QTL) mapping. We outline the usage of a set of PERL scripts that calculate bootstrap estimates of locus-specific heritability of QTL using MERLIN-REGRESS (Abecasis, et al., 2002; Sham, et al. 2002). We assume that users of these scripts have the access to PERL in their computing system.

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