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metal_script.txt
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GENOMICCONTROL ON
OVERLAP ON
TRACKPOSITIONS ON
AVERAGEFREQ ON
MINMAXFREQ ON
OUTFILE hetero_no_overlap_gel_finngenr8_ukbb_jbb_meta_analysis .tbl
MARKERLABEL SNP
ALLELELABELS Allele1 Allele2
PVALUELABEL p.value
EFFECTLABEL BETA
WEIGHTLABEL N
FREQLABEL AF_Allele2
CHROMOSOMELABEL CHR
POSITIONLABEL POS
PROCESS gel_ss_for_metal_b38_cystic.txt
MARKERLABEL SNP
ALLELELABELS ref alt
PVALUELABEL pval
EFFECTLABEL beta
WEIGHTLABEL DONTUSECOLUMN
DEFAULTWEIGHT 341861
FREQLABEL af_alt
CHROMOSOMELABEL chrom
POSITIONLABEL pos
PROCESS finngenr8_cystic_b38_ss.txt
MARKERLABEL SNP
ALLELELABELS hm_other_allele hm_effect_allele
PVALUELABEL p_value
EFFECTLABEL hm_beta
WEIGHTLABEL DONTUSECOLUMN
DEFAULTWEIGHT 534580
FREQLABEL hm_effect_allele_frequency
CHROMOSOMELABEL hm_chrom
POSITIONLABEL hm_pos
PROCESS jbb_ukbb_b38_cystic_ss.tsv
ANALYZE HETEROGENEITY
###########################Using Standard error#############################
SCHEME STDERR
GENOMICCONTROL ON
AVERAGEFREQ ON
MINMAXFREQ ON
OUTFILE stderr_hetero_gel_finngenr8_ukbb_jbb_meta_analysis .tbl
MARKERLABEL SNP
ALLELELABELS Allele1 Allele2
STDERR SE
PVALUELABEL p.value
EFFECTLABEL BETA
WEIGHTLABEL N
FREQLABEL AF_Allele2
PROCESS gel_ss_for_metal_b38_cystic.txt
MARKERLABEL SNP
ALLELELABELS ref alt
STDERR sebeta
PVALUELABEL pval
EFFECTLABEL beta
WEIGHTLABEL DONTUSECOLUMN
DEFAULTWEIGHT 341861
FREQLABEL af_alt
PROCESS finngenr8_cystic_b38_ss.txt
MARKERLABEL SNP
ALLELELABELS hm_other_allele hm_effect_allele
PVALUELABEL p_value
EFFECTLABEL hm_beta
STDERR standard_error
WEIGHTLABEL DONTUSECOLUMN
DEFAULTWEIGHT 534580
FREQLABEL hm_effect_allele_frequency
PROCESS jbb_ukbb_b38_cystic_ss.tsv
ANALYZE HETEROGENEITY
################################################################################
Running without heterogeneity
GENOMICCONTROL ON
OUTFILE basic_analysis_no_hetero_no_overlap_gcystic_b38_meta_analysis .tbl
MARKERLABEL SNP
ALLELELABELS Allele1 Allele2
PVALUELABEL p.value
EFFECTLABEL BETA
WEIGHTLABEL N
FREQLABEL AF_Allele2
CHROMOSOMELABEL CHR
POSITIONLABEL POS
PROCESS gel_ss_for_metal_b38_cystic.txt
MARKERLABEL SNP
ALLELELABELS ref alt
PVALUELABEL pval
EFFECTLABEL beta
WEIGHTLABEL DONTUSECOLUMN
DEFAULTWEIGHT 341861
FREQLABEL af_alt
CHROMOSOMELABEL chrom
POSITIONLABEL pos
PROCESS finngenr8_cystic_b38_ss.txt
MARKERLABEL SNP
ALLELELABELS hm_other_allele hm_effect_allele
PVALUELABEL p_value
EFFECTLABEL hm_beta
WEIGHTLABEL DONTUSECOLUMN
DEFAULTWEIGHT 534580
FREQLABEL hm_effect_allele_frequency
CHROMOSOMELABEL hm_chrom
POSITIONLABEL hm_pos
PROCESS jbb_ukbb_b38_cystic_ss.tsv
ANALYZE
################################################################################
Running stderr without heterogeneity
SCHEME STDERR
GENOMICCONTROL ON
OUTFILE basic_stderr_b38_cystic_meta_analysis .tbl
MARKERLABEL SNP
ALLELELABELS Allele1 Allele2
STDERR SE
EFFECTLABEL BETA
PROCESS gel_ss_for_metal_b38_cystic.txt
MARKERLABEL SNP
ALLELELABELS ref alt
STDERR sebeta
EFFECTLABEL beta
PROCESS finngenr8_cystic_b38_ss.txt
MARKERLABEL SNP
ALLELELABELS hm_other_allele hm_effect_allele
EFFECTLABEL hm_beta
STDERR standard_error
PROCESS jbb_ukbb_b38_cystic_ss.tsv
ANALYZE