WOMBAT – A program for Mixed Model Analyses by Restricted Maximum Likelihood

Example 14 for WOMBAT

This example illustrates automatic' GWAS analysis using WOMBAT for a toy example (simulated data).

• A: Demonstrates run option —-snap. This invokes estimation of SNP effects and their standard errors for (co)variances assumed to be known. In addition to the data, pedigree and parameter file required for 'standard' analyses, it requires a file supplying counts for the number of copies of the reference allele; this has the default name QTLAllels.dat and must be (or a link to it) in the working directory.
The output file QTLSolutions.dat contains estimates of SNP effects, their standard errors and resulting t-values (one per line).
• B: As A, but for a bivariate analysis (2 traits, fit a single SNP).
The output file QTLSolutions.dat contains 6 values per line: estimates of the SNP effects for traits 1 and 2, their standard errors and resulting t-values.
• C: As A, but for two SNPs.
• D: Ditto, but two SNPs & two traits

File RNote_WOMBATSnappy.pdf (included in example14.tar.gz) gives a step by step description.

<bibtex> @Article{km11c,

author =	 {Meyer, K. and Tier, B.},
title =	 {"SNP Snappy": A strategy for fast genome wide
association studies fitting a full mixed model},
year =	 2012,
journal =	 {Genetics},
volume =	 190,
number =	 1,
pages =	 {275--277},
url =		 {http://dx.doi.org/10.1534/genetics.111.134841}`

} </bibtex>