metal_params.example.txt

# This script executes inverse variance weighted fixed effects meta-analysis between GIANT and UK Biobank
# The results for the three phenotypes (whr, whr, whradjwhr) and split by sex (combined, females, males) are stored in the following files:
# ./alignSNPs/ukbb/ukbb.2017.[pheno].[sex].eur.dbsnp151.ukbb.txt and ./alignSNPs/giant/giant.2015.[pheno].[sex].eur.dbsnp151.ukbb.txt
# this is an example of one metal parameters file; there is one needed for each phenotype-sex combination

# Load the input files (one from GIANT and one from UK Biobank)

# Uncomment the next line if you want to apply genomic control
# GENOMICCONTROL ON

# other useful parameters
COLUMNCOUNTING LENIENT
AVERAGEFREQ ON
MINMAXFREQ ON

# run inverse variance weighted fixed effects meta-analysis
SCHEME STDERR

# === DESCRIBE AND PROCESS THE FIRST INPUT FILE ===

SEPARATOR WHITESPACE

MARKER SNP
ALLELE A1 A2
EFFECT beta
STDERR se
PVALUE p
WEIGHT n
FREQ frqA1

# === PROCESS THE FIRST INPUT FILE ===
PROCESS ./alignSNPs/ukbb/ukbb.2017.whr.combined.eur.dbsnp151.ukbb.txt

# === THE SECOND INPUT FILE HAS THE SAME FORMAT, PROCESS ===
PROCESS ./alignSNPs/giant/giant.2015.whr.combined.eur.dbsnp151.ukbb.txt

ANALYZE

QUIT