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 |