GWAMA program





GWAMA: software tool for meta analysis of whole genome association data


Genome-wide association (GWA) studies have proved to be extremely successful in identifying moderate genetic effects contributing to
complex human phenotypes. However, to gain insights into increasingly more modest signals of association, samples of many thousands
of individuals are required. One approach to overcome this problem is to combine the results of GWA studies from closely related
populations via meta-analysis, without direct exchange of genotype and phenotype data.

We have developed the GWAMA (Genome-Wide Association Meta Analysis) software to perform meta-analysis of the results of GWA studies
of binary or quantitative phenotypes. Fixed- and random-effect meta-analyses are performed for both directly genotyped and imputed SNPs using
estimates of the allelic odds ratio and 95% confidence interval for binary traits, and estimates of the allelic effect size and
standard error for quantitative phenotypes. GWAMA can be used for analysing the results of all different genetic models (multiplicative,
additive, dominant, recessive). The software incorporates error trapping facilities to identify strand alignment errors and allele flipping,
and performs tests of heterogeneity of effects between studies.

Magi R, Morris AP: GWAMA: software for genome-wide association meta-analysis. BMC Bioinformatics 2010, 11:288. (link)

Magi R, Lindgren CM, Morris AP: Meta-analysis of sex-specific genome-wide association studies. Genetic Epidemiology 2010, 34(8):846-853. (link)