cambridge-ceu / METAL

Meta-analysis of genomewide association scans

METAL

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.

Requirements

• CMake cross-platform make system

Compilation

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

The compiled metal executable will be installed into build/bin directory.

New features

• 2020-05-05

  • Implemented new options EFFECT_PRINT_PRECISION and STDERR_PRINT_PRECISION to control print precision of Effect and StdErr output columns, correspondingly. For example, setting EFFECT_PRINT_PRECISION 12 will force METAL to print 12 digits after the decimal point in the Effect column. The default is to print 4 digits after the decimal point for both Effect and StdErr. Increasing precision is useful when you plan to use Effect and StdErr values computed by METAL in other downstream analyses.

• 2018-08-28

  • Implemented new option TRACKPOSITIONS. If enabled, METAL checks if chromosome and position of a variant match across studies. The Chromosome and Position fields are propagated to the meta-analysis result file (useful when generating Manhattan or LocusZoom plots).

• 2017-12-21

  • 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

Documentation

Complete documentation is available at https://genome.sph.umich.edu/wiki/METAL_Documentation.