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.