Table 2 |
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|
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 |
|
|
||||
|
Mägi and Morris BMC Bioinformatics 2010 11:288 doi:10.1186/1471-2105-11-288 |
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