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Table 2 Comparison of software packages for genome-wide meta-analysis of association summary statistics.

From: GWAMA: software for genome-wide association meta-analysis

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