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 = 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.
http://www.geenivaramu.ee/en/tools/gwama
GWAMA was written by Reedik Magi and Andrew P Morris.