QTLSNP: Exploratory SNP analysis for Quantitative Traits

Description: qtlsnp displays summary results for SNP analysis of quantitative traits.  It succinctly reports on multiple SNPs and trait variables. Optionally qtlsnp reports details for each SNP analyzed.

By default, qtlsnp uses linear regression to compare the equality of means across genotypes while allowing for covariate adjustment. By specifying the median option, qtlsnp uses median regression instead of linear regression (see help for qreg), and by specifying bs, qtlsnp uses median regression with bootstrapped VCE (see help for bsqreg).

qtlsnp assumes a codominant genetic model and test for an additive effect, a dominant effect and that both effects are equal to zero (This last comparison is equivalent to comparing means across the three possible genotypes). The dominant and recessive options are used to modify this assumption.  For example, if the three possible genotypes at a given SNP are cc, ct, and tt, The dominant option tells qtlsnp to combines the cc and ct genotypes and compare the quantitative mean trait value for these combine genotypes against the mean of the tt genotype. The recessive option combines the ct and tt genotypes and qtlsnp compares the quantitative mean trait value for these combined genotypes against the mean of the cc genotype. Note that the terms dominant and recessive are arbitrary labels.

Reference: 

If you use this program please reference:

Cleves MA. Exploratory Analysis of Single Nucleotide Polymorphisms (SNP) for Quantitative Traits. The Stata Journal. 5(2):141–153 (2005). (Download)

 and optionally the website:

http://www.biostat-resources.com/stata/