METAL is a tool for the meta-analysis of genome-wide association studies. More information about METAL is available at https://genome.sph.umich.edu/wiki/METAL.
Download and unarchive latest stable version of METAL source code or clone this GitHub repository to obtain development version. Then execute the following commands inside the directory with METAL source code:
mkdir build && cd build cmake -DCMAKE_BUILD_TYPE=Release .. make make test make install
metal executable will be installed into
STDERR_PRINT_PRECISIONto control print precision of
StdErroutput columns, correspondingly. For example, setting
EFFECT_PRINT_PRECISION 12will force METAL to print 12 digits after the decimal point in the
Effectcolumn. The default is to print 4 digits after the decimal point for both
StdErr. Increasing precision is useful when you plan to use
StdErrvalues computed by METAL in other downstream analyses.
TRACKPOSITIONS. If enabled, METAL checks if chromosome and position of a variant match across studies. The
Positionfields are propagated to the meta-analysis result file (useful when generating Manhattan or LocusZoom plots).
Correction for sample overlap in sample size weighted meta-analysis (developed by Sebanti Sengupta). First, METAL estimates the number of individuals that are common among two or more studies based on Z-statistics from each study. Then, METAL adjusts for sample overlap when calculating overall Z-statistics by correcting the weights with the estimated number of individuals in common.
To enable correction for sample overlap in your sample size weighted meta-analysis, use
OVERLAP ON command (valid only with
SCHEME SAMPLESIZE) before any
PROCESS commands. By default, METAL uses Z-statistics <1 for esimating the number of individuals that are common among studies. To change this threshold, use
ZCUTOFF [number] command. The
N column in the result file will store sample size corrected for overlap between studies.
More information on this specific method can be found on our wiki: https://genome.sph.umich.edu/wiki/METAL_Documentation#Sample_Overlap_Correction
Complete documentation is available at https://genome.sph.umich.edu/wiki/METAL_Documentation.