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GWAMA - Genome-Wide Association Meta Analysis

GWAMA(1) General Commands Manual GWAMA(1)

NAME

GWAMA - Genome-Wide Association Meta Analysis

SYNOPSIS

GWAMA [ options]

DESCRIPTION

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.

OPTIONS

-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 = 1
--no_alleles
No allele information has been given. Expecting always the same EA.
--indel_alleles
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).
--filter
Set a filtering based on column header. It needs 3 arguments: column name, equation [>,<,>=,<=,==,!=], filter value. Multiple filters can be set.
--name_marker
Alternative header to marker name col.
--name_strand
Alternative header to strand column.
--name_n
Alternative header to sample size col.
--name_ea
Alternative header to effect allele column.
--name_nea
Alternative header to non-effect allele column.
--name_eaf
Alternative header to effect allele frequency column.
--name_beta
Alternative header to beta column.
--name_se
Alternative header to std. err. col.
--name_or
Alternative header to OR column.
--name_or_95l
Alternative header to OR 95L column.
--name_or_95u
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.

SEE ALSO

http://www.geenivaramu.ee/en/tools/gwama

AUTHOR

GWAMA was written by Reedik Magi and Andrew P Morris.
 
August 2016 2.2.2