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GWAMA - Online in the Cloud

Run GWAMA in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command GWAMA that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



GWAMA - Genome-Wide Association Meta Analysis


GWAMA [options]


GWAMA (Genome-Wide Association Meta Analysis) software performs 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.


-i, --filelist=filename
Specify studies' result files. Default = gwama.in

-o, --output=fileroot
Specify file root for output of analysis. Default = gwama (gwama.out, gwama.gc.out)

-r, --random
Use random effect correction. Default = disabled

-gc, --genomic_control
Use genomic control for adjusting studies' result files. Default = disabled

-gco, --genomic_control_output
Use genomic control on meta-analysis summary (i.e. results of meta- analysis are
corrected for gc). Default = disabled

-qt, --quantitative
Select quantitative trait version (BETA and SE columns). Default = binary trait

-m, --map=filename
Select file name for marker map.

-t, --threshold=0-1
The p-value threshold for showing direction in summary effect directions. Default =

No allele information has been given. Expecting always the same EA.

Allele labes might contain more than single letter. No strand checks.

--sex Run gender-differentiated and gender- heterogeneity analysis (method described in
paper Magi, Lindgren & Morris 2010). Gender info must be provided in filelist file.
(second column after file names is either M or F).

Alternative header to marker name col.

Alternative header to strand column.

Alternative header to sample size col.

Alternative header to effect allele column.

Alternative header to non-effect allele column.

Alternative header to effect allele frequency column.

Alternative header to beta column.

Alternative header to std. err. col.

Alternative header to OR column.

Alternative header to OR 95L column.

Alternative header to OR 95U column.

-h, --help
Print this help.

-v, --version
Print GWAMA version number. This manual page must be insufficient. Please use the
help option for a quick reminder of the options of gwama or turn to its home page
with the online documentation or the downloadable manual.

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