GWAMA tutorial | University of Tartu Institute of Genomics

Contacts of UT units

Faculty of Arts and Humanities
Faculty phone: 
+372 737 5341
Faculty address: 
Jakobi 2, rooms 116–121, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5341
    Faculty address: 
    Jakobi 2, rooms 116–121, 51005 Tartu
  • Institute of History and Archaeology
    Faculty phone: 
    +372 737 5651
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Estonian and General Linguistics
    Faculty phone: 
    +372 737 5221
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Philosophy and Semiotics
    Faculty phone: 
    +372 737 5314
    Faculty address: 
    Jakobi 2, rooms 309–352, 51005 Tartu
  • Institute of Cultural Research
    Faculty phone: 
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    Faculty address: 
    Ülikooli 16, 51003 Tartu
  • School of Theology and Religious Studies
    Faculty phone: 
    +372 737 5301
    Faculty address: 
    Ülikooli 18–310, 50090 Tartu
  • College of Foreign Languages and Cultures
    Faculty address: 
    Lossi 3, 51003 Tartu
  • Viljandi Culture Academy
    Faculty phone: 
    +372 435 5232
    Faculty address: 
    Posti 1, 71004 Viljandi
Faculty of Social Sciences
Faculty phone: 
+372 737 5957
Faculty address: 
Lossi 36, 51003 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5900
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Institute of Education
    Faculty phone: 
    +372 737 6440
    Faculty address: 
    Salme 1a–29, 50103 Tartu
  • Johan Skytte Institute of Political Studies
    Faculty phone: 
    +372 737 5582
    Faculty address: 
    Lossi 36–301, 51003 Tartu
  • School of Economics and Business Administration
    Faculty phone: 
    +372 737 6310
    Faculty address: 
    J. Liivi 4, 50409 Tartu
  • Institute of Psychology
    Faculty phone: 
    +372 737 5902
    Faculty address: 
    Näituse 2, 50409 Tartu
  • School of Law
    Faculty phone: 
    +372 737 5390
    Faculty address: 
    Näituse 20–324, 50409 Tartu
  • Institute of Social Studies
    Faculty phone: 
    +372 737 5188
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Narva College
    Faculty phone: 
    +372 740 1900
    Faculty address: 
    Raekoja plats 2, 20307 Narva
  • Pärnu College
    Faculty phone: 
    +372 445 0520
    Faculty address: 
    Ringi 35, 80012 Pärnu
Faculty of Medicine
Faculty phone: 
+372 737 5326
Faculty address: 
Ravila 19, 50411 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5326
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Biomedicine and Translational Medicine
    Faculty phone: 
    +372 737 4210
    Faculty address: 
    Biomeedikum, Ravila 19, 50411 Tartu
  • Institute of Pharmacy
    Faculty phone: 
    +372 737 5286
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Dentistry
    Faculty phone: 
    +372 731 9856
    Faculty address: 
    Raekoja plats 6, 51003 Tartu
  • Institute of Clinical Medicine
    Faculty phone: 
    +372 737 5323
    Faculty address: 
    L. Puusepa 8, 50406 Tartu
  • Institute of Family Medicine and Public Health
    Faculty phone: 
    +372 737 4190
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Sport Sciences and Physiotherapy
    Faculty phone: 
    +372 737 5360
    Faculty address: 
    Jakobi 5–205, 51005 Tartu
Faculty of Science and Technology
Faculty phone: 
+372 737 5820
Faculty address: 
Vanemuise 46–208, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5820
    Faculty address: 
    Vanemuise 46–208, 51005 Tartu
  • Institute of Computer Science
    Faculty phone: 
    +372 737 5445
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Estonian Marine Institute
    Faculty phone: 
    +372 671 8902
    Faculty address: 
    Mäealuse 14, 12618 Tallinn
  • Institute of Physics
    Faculty address: 
    W. Ostwaldi 1, 50411 Tartu
  • Institute of Chemistry
    Faculty phone: 
    +372 737 5261
    Faculty address: 
    Ravila 14a, 50411 Tartu
  • Institute of Mathematics and Statistics
    Faculty phone: 
    +372 737 5860
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Institute of Molecular and Cell Biology
    Faculty phone: 
    +372 737 5011
    Faculty address: 
    Riia 23, 23b–134, 51010 Tartu
  • Tartu Observatory
    Faculty phone: 
    +372 737 4510
    Faculty address: 
    Observatooriumi 1, Tõravere, 61602 Tartumaa
  • Institute of Technology
    Faculty phone: 
    +372 737 4800
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Ecology and Earth Sciences
    Faculty phone: 
    +372 737 5835
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Institutions
  • Library
    Faculty phone: 
    +372 737 5702
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Youth Academy
    Faculty phone: 
    +372 737 5581
    Faculty address: 
    Uppsala 10, 51003 Tartu
  • Institute of Genomics
    Faculty phone: 
    +372 737 4000
    Faculty address: 
    Riia 23b, 51010 Tartu
  • Museum
    Faculty phone: 
    +372 737 5674
    Faculty address: 
    Lossi 25, 51003 Tartu
  • University of Tartu Natural History Museum and Botanical Garden
    Faculty phone: 
    +372 737 6076
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Support Units
  • Administrative Office
    Faculty phone: 
    +372 737 5606
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Centre for Entrepreneurship and Innovation
    Faculty phone: 
    +372 737 6339
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • University Office in Tallinn
    Faculty phone: 
    +372 737 6600
    Faculty address: 
    Teatri väljak 3, 10143 Tallinn
  • Estates Office
    Faculty phone: 
    +372 737 5137
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Finance Office
    Faculty phone: 
    +372 737 5125
    Faculty address: 
    Jakobi 4, 51005 Tartu
  • Grant Office
    Faculty phone: 
    +372 737 6215
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • Information Technology Office
    Faculty phone: 
    +372 737 6000, IT-help: +372 737 5500
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Human Resources Office
    Faculty phone: 
    +372 737 5145
    Faculty address: 
    Ülikooli 18, rooms 302 and 304, 50090 Tartu
  • Internal Audit Office
    Faculty address: 
    Ülikooli 17–103, 51005 Tartu
  • Marketing and Communication Office
    Faculty phone: 
    +372 737 5687
    Faculty address: 
    Ülikooli 18, rooms 102, 104, 209, 210, 50090 Tartu
  • Office of Academic Affairs
    Faculty phone: 
    +372 737 5620
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Procurement Office
    Faculty phone: 
    +372 737 6632
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Rector's Strategy Office
    Faculty phone: 
    +372 737 5600
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Student Council
    Faculty phone: 
    +372 737 5400
    Faculty address: 
    Ülikooli 18b, 51005 Tartu
Other Units
  • University of Tartu Academic Sports Club
    Faculty phone: 
    +372 737 5371
    Faculty address: 
    Ujula 4, 51008 Tartu
  • Tartu Student Village
    Faculty phone: 
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    Faculty address: 
    Narva mnt 25, 51013 Tartu
  • Tartu Students’ Club
    Faculty phone: 
    +372 730 2400
    Faculty address: 
    Kalevi 24, 51010 Tartu
  • University of Tartu Press
    Faculty phone: 
    +372 737 5945
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Tartu University Hospital
    Faculty address: 
    L. Puusepa 1a, 50406 Tartu
  • University of Tartu Foundation
    Faculty phone: 
    +372 737 5852
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • View all other units

Contacts of UT units

Faculty of Arts and Humanities
Faculty phone: 
+372 737 5341
Faculty address: 
Jakobi 2, rooms 116–121, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5341
    Faculty address: 
    Jakobi 2, rooms 116–121, 51005 Tartu
  • Institute of History and Archaeology
    Faculty phone: 
    +372 737 5651
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Estonian and General Linguistics
    Faculty phone: 
    +372 737 5221
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Philosophy and Semiotics
    Faculty phone: 
    +372 737 5314
    Faculty address: 
    Jakobi 2, rooms 309–352, 51005 Tartu
  • Institute of Cultural Research
    Faculty phone: 
    (+372) 737 5223
    Faculty address: 
    Ülikooli 16, 51003 Tartu
  • School of Theology and Religious Studies
    Faculty phone: 
    +372 737 5301
    Faculty address: 
    Ülikooli 18–310, 50090 Tartu
  • College of Foreign Languages and Cultures
    Faculty address: 
    Lossi 3, 51003 Tartu
  • Viljandi Culture Academy
    Faculty phone: 
    +372 435 5232
    Faculty address: 
    Posti 1, 71004 Viljandi
Faculty of Social Sciences
Faculty phone: 
+372 737 5957
Faculty address: 
Lossi 36, 51003 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5900
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Institute of Education
    Faculty phone: 
    +372 737 6440
    Faculty address: 
    Salme 1a–29, 50103 Tartu
  • Johan Skytte Institute of Political Studies
    Faculty phone: 
    +372 737 5582
    Faculty address: 
    Lossi 36–301, 51003 Tartu
  • School of Economics and Business Administration
    Faculty phone: 
    +372 737 6310
    Faculty address: 
    J. Liivi 4, 50409 Tartu
  • Institute of Psychology
    Faculty phone: 
    +372 737 5902
    Faculty address: 
    Näituse 2, 50409 Tartu
  • School of Law
    Faculty phone: 
    +372 737 5390
    Faculty address: 
    Näituse 20–324, 50409 Tartu
  • Institute of Social Studies
    Faculty phone: 
    +372 737 5188
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Narva College
    Faculty phone: 
    +372 740 1900
    Faculty address: 
    Raekoja plats 2, 20307 Narva
  • Pärnu College
    Faculty phone: 
    +372 445 0520
    Faculty address: 
    Ringi 35, 80012 Pärnu
Faculty of Medicine
Faculty phone: 
+372 737 5326
Faculty address: 
Ravila 19, 50411 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5326
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Biomedicine and Translational Medicine
    Faculty phone: 
    +372 737 4210
    Faculty address: 
    Biomeedikum, Ravila 19, 50411 Tartu
  • Institute of Pharmacy
    Faculty phone: 
    +372 737 5286
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Dentistry
    Faculty phone: 
    +372 731 9856
    Faculty address: 
    Raekoja plats 6, 51003 Tartu
  • Institute of Clinical Medicine
    Faculty phone: 
    +372 737 5323
    Faculty address: 
    L. Puusepa 8, 50406 Tartu
  • Institute of Family Medicine and Public Health
    Faculty phone: 
    +372 737 4190
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Sport Sciences and Physiotherapy
    Faculty phone: 
    +372 737 5360
    Faculty address: 
    Jakobi 5–205, 51005 Tartu
Faculty of Science and Technology
Faculty phone: 
+372 737 5820
Faculty address: 
Vanemuise 46–208, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5820
    Faculty address: 
    Vanemuise 46–208, 51005 Tartu
  • Institute of Computer Science
    Faculty phone: 
    +372 737 5445
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Estonian Marine Institute
    Faculty phone: 
    +372 671 8902
    Faculty address: 
    Mäealuse 14, 12618 Tallinn
  • Institute of Physics
    Faculty address: 
    W. Ostwaldi 1, 50411 Tartu
  • Institute of Chemistry
    Faculty phone: 
    +372 737 5261
    Faculty address: 
    Ravila 14a, 50411 Tartu
  • Institute of Mathematics and Statistics
    Faculty phone: 
    +372 737 5860
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Institute of Molecular and Cell Biology
    Faculty phone: 
    +372 737 5011
    Faculty address: 
    Riia 23, 23b–134, 51010 Tartu
  • Tartu Observatory
    Faculty phone: 
    +372 737 4510
    Faculty address: 
    Observatooriumi 1, Tõravere, 61602 Tartumaa
  • Institute of Technology
    Faculty phone: 
    +372 737 4800
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Ecology and Earth Sciences
    Faculty phone: 
    +372 737 5835
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Institutions
  • Library
    Faculty phone: 
    +372 737 5702
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Youth Academy
    Faculty phone: 
    +372 737 5581
    Faculty address: 
    Uppsala 10, 51003 Tartu
  • Institute of Genomics
    Faculty phone: 
    +372 737 4000
    Faculty address: 
    Riia 23b, 51010 Tartu
  • Museum
    Faculty phone: 
    +372 737 5674
    Faculty address: 
    Lossi 25, 51003 Tartu
  • University of Tartu Natural History Museum and Botanical Garden
    Faculty phone: 
    +372 737 6076
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Support Units
  • Administrative Office
    Faculty phone: 
    +372 737 5606
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Centre for Entrepreneurship and Innovation
    Faculty phone: 
    +372 737 6339
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • University Office in Tallinn
    Faculty phone: 
    +372 737 6600
    Faculty address: 
    Teatri väljak 3, 10143 Tallinn
  • Estates Office
    Faculty phone: 
    +372 737 5137
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Finance Office
    Faculty phone: 
    +372 737 5125
    Faculty address: 
    Jakobi 4, 51005 Tartu
  • Grant Office
    Faculty phone: 
    +372 737 6215
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • Information Technology Office
    Faculty phone: 
    +372 737 6000, IT-help: +372 737 5500
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Human Resources Office
    Faculty phone: 
    +372 737 5145
    Faculty address: 
    Ülikooli 18, rooms 302 and 304, 50090 Tartu
  • Internal Audit Office
    Faculty address: 
    Ülikooli 17–103, 51005 Tartu
  • Marketing and Communication Office
    Faculty phone: 
    +372 737 5687
    Faculty address: 
    Ülikooli 18, rooms 102, 104, 209, 210, 50090 Tartu
  • Office of Academic Affairs
    Faculty phone: 
    +372 737 5620
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Procurement Office
    Faculty phone: 
    +372 737 6632
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Rector's Strategy Office
    Faculty phone: 
    +372 737 5600
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Student Council
    Faculty phone: 
    +372 737 5400
    Faculty address: 
    Ülikooli 18b, 51005 Tartu
Other Units
  • University of Tartu Academic Sports Club
    Faculty phone: 
    +372 737 5371
    Faculty address: 
    Ujula 4, 51008 Tartu
  • Tartu Student Village
    Faculty phone: 
    +372 740 9959
    Faculty address: 
    Narva mnt 25, 51013 Tartu
  • Tartu Students’ Club
    Faculty phone: 
    +372 730 2400
    Faculty address: 
    Kalevi 24, 51010 Tartu
  • University of Tartu Press
    Faculty phone: 
    +372 737 5945
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Tartu University Hospital
    Faculty address: 
    L. Puusepa 1a, 50406 Tartu
  • University of Tartu Foundation
    Faculty phone: 
    +372 737 5852
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • View all other units

GWAMA tutorial

INTRODUCTION

GWAMA (Genome-Wide Association Meta Analysis) software has been developed to perform meta-analysis of the results of GWA studies of binary or quantitative phenotypes. The software incorporates error trapping facilities to identify strand alignment errors and allele flipping, and performs tests of heterogeneity of effects between studies.

INSTALLATION (UNIX)

Copy gwama.zip file into your computer, unzip the file:

unzip gwama.zip

To compile GWAMA program, use command:

make

in the folder where files have been unpacked. The program can be run by typing:

GWAMA

INSTALLATION (WINDOWS)

Copy gwama.zip file into your computer and unpack the *.msi file.

Double-click on the *.msi file and follow the installation instructions.

The program can be run by typing:

c:\Program Files\WTCHG\gwama\gwama (if installed into default folder)
In case of any questions or comments please dont hesitate to contact the authors.
 

INPUT FILES

For running GWAMA you have to create an input file (default name “gwama.in”), which contains the list of all study files. The should have each results' file on separate row. If genderwise heterogeneity analysis option is used, second column should identify if the cohort contains males (M) or females (F) data.

Sample “gwama.in” file:

Pop1.txt M
Pop2.txt M
Pop3.txt F

 

Each GWA study file has mandatory column headers:

1) MARKERNAME – snp name

2) EA – effect allele

3) NEA – non effect allele

4) OR - odds ratio

5) OR_95L - lower confidence interval of OR

6) OR_95U - upper confidence interval of OR

In case of quantitative trait:

4) BETA – beta

5) SE – std. error

Study files might also contain columns:

7) N - number of samples

8) EAF – effect allele frequency

9) STRAND – marker strand (if the column is missing then program expects all markers being on positive strand)

10) IMPUTED – if marker is imputed or not (if the column is missing then all markers are counted as directly genotyped ones)

 

Sample study file (NB! This file is a quantitative trait one and GWAMA has to be run with -qt command line option):

MARKERNAME STRAND CHR POS IMP EA NEA BETA SE
rs12565286 + 1 761153 0 G C -0.02 0.0403
rs2977670 + 1 763754 0 C G -0.01 0.40612
rs12138618 + 1 790098 0 G A -0.07 0.37
rs3094315 + 1 792429 0 G A 0.0258 0.1012
rs3131968 + 1 794055 0 G A -0.373 0.0101
rs2519016 + 1 805811 0 T C 0.26 0.3472
rs12562034 + 1 808311 0 G A 0.0092 0.2


Input files must be either tab or space delimited. Files must not have empty columns as multiple separators are treated as one. Files may contain additional columns, which are not used by GWAMA.

RUNNING GWAMA

Command line options:

GWAMA

--filelist {filename} or -i {filename} Specify studies' result files. Default = gwama.in

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

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

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

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

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

--map {filename} or -m {filename} Select file name for marker map.

--threshold {0-1} or -t {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).

--name_marker alternative header to marker name column

--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

--help or -h Print this help

--version or -v Print GWAMA version number
 

OUTPUT FILES

GWAMA generates following output files:

gwama.out (or 'fileroot'.out if --output option is used)
This file contains results of meta-analysis. Output file has following columns:

chromosome - Marker chromosome
position - Marker position (bp)
rs_number - Marker ID
reference_allele - Effect allele
other_allele - Non effect allele

OR - Overall odds ratio for meta-analysis
OR_95L - Lower 95% CI for OR
OR_95U - Upper 95% CI for OR

IN CASE OF QUANTITATIVE TRAIT (-qt)
beta - Overall beta value for meta-analysis
beta_95L - Lower 95% CI for BETA
beta_95U - Upper 95% CI for BETA

z - Z-score
p-value - Meta-analysis p-value
-log10_p-value - Absolut value of logarithm of meta-analysis p-value to the base of 10.
q_statistic - Cochran's heterogeneity statistic
q_p-value - Cochran's heterogeneity statistic's p-value
i2 - Heterogeneity index I2 by Higgins et al 2003
n_studies - Number of studies with marker present
n_samples - Number of samples with marker present (will be NA if marker is present in any input file where N column is not present)
effects - Summary of effect directions ('+' - positive effect of reference allele, '-' - negative effect of reference allele, '0' - no effect (or non-significant) effect of reference allele, '?' - missing data)

gwama.gc.out (or 'fileroot'.gc.out if --output option is used)
This file contains lambda values for GC correction. The file is only generated, if -gc oprion is used.

gwama.log.out
This file contains all log information about current GWAMA run. Each error and warning has unique error code. More information for them can be found from gwama.err.out file.

gwama.err.out
This file contains all errors and warning generated during GWAMA run. Information about any error can be searched according to error code. For example in UNIX:
grep E000000001 gwama.err.out
gives information about error E000000001

GENDER SPECIFIC ANALYSIS

If gender specific analysis option is used, additional columns will appear into output file. All male_ and female_ columns are calculated using cohorts with defined gender.

male_eaf
male_OR (or beta if quantitative trait is analysed)
male_OR_se
male_OR_95L
male_OR_95U
male_z
male_p-value
male_n_studies
male_n_samples
female_eaf
female_OR
female_OR_se
female_OR_95L
female_OR_95U
female_z
female_p-value
female_n_studies
female_n_samples
gender_differentiated_p-value - combined p-value of males and females assuming different effect sizes between genders (2 degrees of freedom)
gender_heterogeneity_p-value - heterogeneity between genders (1 degree of freedom)

Paper describing gender specific analysis framework has beed submitted.

CREATING PLOTS

Manhattan and QQ plots can be created with accompanied R scripts.

R --slave --vanilla < MANH.R

R --slave --vanilla < QQ.R

By default they expect input file name "gwama.out" and they create output files: "gwama.out.qq.png" and "gwama.out.manh.png". Different names can be used as:

R --slave --vanilla --args input=inputfilename out=outputfilename < QQ.R

Manhattan plot can be drawn, if chromosomal position have been added to the file (for example command line: --map hapmap35.map)

R version 2.9.0 or later must be used with png support

CITING REFERENCES

Magi R, Morris AP: GWAMA: software for genome-wide association meta-analysis. BMC Bioinformatics 2010, 11:288.

Magi R, Lindgren CM, Morris AP: Meta-analysis of sex-specific genome-wide association studies. Genetic Epidemiology 2010, 34(8):846-853.