option to estimate a genomic control parameter (Devlin and Roeder, 1999) for each input file and apply an appropriate genomic control correction to input statistics prior to performing meta-analysis. To facilitate the detection of allele labels that may have been mis-specified by the user, which is critical for the correct determination of the direction of effect, METAL implements an option to output the mean, variance and minimum and maximum allele frequencies for each marker. METAL will track custom statistics, such as cumulative sample size, even when the standard error-weighted meta-analysis was performed. METAL can read gzipped files to allow for efficient use of disk space and optionally allows for subsets of markers to be analyzed. Full documentation of all options is available at http://www.sph.umich.edu/csg/abecasis/metal/.
