Provided by: gwama_2.1+dfsg-2_amd64 bug


       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 =

       -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.



       GWAMA was written by Reedik Magi and Andrew P Morris.

       This manual page was written by Dylan Aïssi <>, for the Debian project
       (but may be used by others).