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LDSCcoms.txt
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LDSCcoms.txt
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###### Heritability and genetic correlation coms ##########################
#LDSC intercept and lambda for full meta-analysis
munge_sumstats.py --out mvGWAMAmeta --sumstats mvGWAMAmeta.txt --N-col Neff --snp SNP --a1 a1 --a2 a2 --p p --merge-alleles w_hm3.snplist
#heritability
# META-ANALYSIS (excluding UKB)
#see mvGWAMAcoms.txt
munge_sumstats.py --out mvGWAMAnoUKB --sumstats mvGWAMAnoUKB.txt --N-col Neff --snp SNP --a1 a1 --a2 a2 --p p --merge-alleles w_hm3.snplist
ldsc.py --h2 mvGWAMAnoUKB.sumstats.gz --ref-ld-chr eur_w_ld_chr/ --w-ld-chr eur_w_ld_chr/ --samp-prev 0.0574041885 --pop-prev 0.05 --out mvGWAMAnoUKBh2
#rg between UKB excluded meta-analysis results and UKB data
munge_sumstats.py --out UKB --sumstats ukb.txt --N-col NMISS --snp SNP --a1 A1 --a2 A2 --p P --merge-alleles w_hm3.snplist
ldsc.py --rg mvGWAMAnoUKB.sumstats.gz,UKB.sumstats.gz --ref-ld-chr eur_w_ld_chr/ --w-ld-chr eur_w_ld_chr/ --out UKBvsrestRG