Table 2

Comparison of software packages for genome-wide meta-analysis of association summary statistics.

Software package

METAL

MetABEL

META

GWAMA


Pre-processing of GWA analysis files

No

*ABEL

SNPTEST

SNPTEST, PLINK


Strand flipping for aligning effect directions

Yes

Yes

Yes

Yes


Fixed effect analysis

Yes

Yes

Yes

Yes


Random effect analysis

No

No

Yes

Yes


Heterogeneity statistics (Cochran's Q statistic, I2)

Q

No

Q, I2

Q, I2


Automated genomic control for population structure

Yes

Yes

Yes

Yes


Graphical visualisation of meta-analysis results

No

Forest plot

No

Separate scripts for Manhattan and QQ plots


M├Ągi and Morris BMC Bioinformatics 2010 11:288   doi:10.1186/1471-2105-11-288

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