### required input: GWAS result files (in this case: output from nf-gwas)

# This runs several independent meta-analyses at once


# First meta-analysis, main model, all 
# specify the options for the first metal run
 
# First meta-analysis, main model, all 
# specify the options for the first metal run
SCHEME STDERR
MARKER ID_HARMONIZED
ALLELE ALLELE1 ALLELE0
AVERAGEFREQ ON
FREQLABEL A1FREQ
EFFECT BETA
STDERR SE
SEPARATOR  TAB
CUSTOMVARIABLE TotalN
TRACKPOSITIONS ON
CHROMOSOMELABEL CHROM
POSITIONLABEL GENPOS

LABEL TotalN as N

PROCESS ../KORAF3.APOA4invnorm.all.basic.regenie.gz
PROCESS ../KORAF4.APOA4invnorm.all.basic.regenie.gz
PROCESS ../COLAUS.APOA4invnorm.all.basic.regenie.gz
PROCESS ../AugUR1.APOA4invnorm.all.basic.regenie.gz
PROCESS ../AugUR2.APOA4invnorm.all.basic.regenie.gz
PROCESS ../YFS.APOA4invnorm.all.basic.regenie.gz
PROCESS ../Diagene.APOA4invnorm.all.basic.regenie.gz
PROCESS ../RS1/Rotterdam.APOA4invnorm.all.basic.regenie.gz
PROCESS ../RS2/Rotterdam.APOA4invnorm.all.basic.regenie.gz

# specify name for output file
# Attention: leave one space between name and suffix
OUTFILE ApoA4_invnorm_metaanalysis_all_basic_withoutGCKD_ .tbl
MINWEIGHT 5000
ANALYZE HETEROGENEITY
CLEAR
# after CLEAR a complete new run of metal can be started


QUIT