The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.
Version
2009-01-12
Sample Sessions
First login to helix. Replace 'user' in the following example with user's helix ID. Create a directory called /home/user/metal
The 'metal' binary is located at /usr/local/metal/
The sample files GlucoseExample.tar can be copied from /usr/local/metal/examples
First copy the sample files to /home/user/metal, unzip file:
% cd /home/user/metal
% cp /usr/local/metal/examples/GlucoseExample.tar .
% tar xvf GlucoseExample.tar
% cd GlucoseExample
% mv MAGIC_FUSION_Results.txt.gz MAGIC_FUSION_Results.txt
% /usr/local/metal/metal << EOT
MARKER SNP
WEIGHT N
ALLELE EFFECT_ALLELE NON_EFFECT_ALLELE
FREQ EFFECT_ALLELE_FREQ
EFFECT BETA
STDERR SE
PVAL P_VAL
PROCESS DGI_three_regions.txt
MARKER SNP
ALLELE EFFECT_ALLELE NON_EFFECT_ALLELE
FREQ FREQ_EFFECT
WEIGHT N
EFFECT BETA
STDERR SE
PVAL PVALUE
PROCESS MAGIC_FUSION_Results.txt
MARKER SNP
DEFAULT 4108
ALLELE AL1 AL2
FREQ FREQ1
EFFECT EFFECT
STDERR SE
PVAL PVALUE
PROCESS magic_SARDINIA.tbl
ANALYZE
Press Ctrl-D to submit these commands. Two output files will be created.Documentation
http://www.sph.umich.edu/csg/abecasis/Metal/download/metal-instructions.pdf
