METAL Glucose Example Script

# This file includes a series of comments. Each comment is marked 
# by a # character as the first character in the line.
#
# This is a comment!

# Meta-analysis weighted by standard error does not work well
# when different studies used very different transformations.
# In this case, some attempt was made to use similar trait
# transformation and you can request a standard error based
# analysis by uncommenting the following line:
# SCHEME   STDERR

# Usually, it is a good to apply genomic control to each
# input file. However, in this example, all the markers being
# examined reside in strongly associated loci and it probably 
# is not a good idea. To find out what happens if you turn
# on genomic control, uncomment the following line.
# GENOMICCONTROL ON

# To help identify allele flips, it can be useful to track
# allele frequencies in the meta-analysis. To enable this
# capability, uncomment the following two lines.
# AVERAGEFREQ ON
# MINMAXFREQ ON

# To restric meta-analysis to two previously reported SNPs
# and summarize study specific results, uncomment the two
# lines that follow.
# ADDFILTER SNP IN (rs10830963,rs563694)
# VERBOSE ON

# Describe and process the DGI input files
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

# Describe and process the FUSION input files
MARKER   SNP
ALLELE   EFFECT_ALLELE NON_EFFECT_ALLELE
FREQ     FREQ_EFFECT
WEIGHT   N
EFFECT   BETA
STDERR   SE
PVAL     PVALUE

PROCESS MAGIC_FUSION_Results.txt.gz

# Describe and process the SardiNIA input files
MARKER   SNP
DEFAULT  4106
ALLELE   AL1 AL2
FREQ     FREQ1
EFFECT   EFFECT
STDERR   SE
PVAL     PVALUE

PROCESS magic_SARDINIA.tbl

# Execute meta-analysis
ANALYZE