ldsc_script

munge_sumstats.py --sumstats pgc.cross.SCZ17.2013-05.txt --N 17115 --out scz --merge-alleles w_hm3.snplist

munge_sumstats.py --sumstats pgc.cross.BIP11.2013-05.txt --N 11810 --out bip --merge-alleles w_hm3.snplist

# LD Score Regression
ldsc.py --rg scz.sumstats.gz,bip.sumstats.gz --ref-ld-chr eur_w_ld_chr/ --w-ld-chr eur_w_ld_chr/ --out scz_bip less scz_bip.log

ldsc.py --h2 scz.sumstats.gz --ref-ld-chr eur_w_ld_chr/ --w-ld-chr eur_w_ld_chr/ --out scz_h2
ldsc.py --h2 bip.sumstats.gz --ref-ld-chr eur_w_ld_chr/ --w-ld-chr eur_w_ld_chr/ --out bip_h2
less scz_h2.log

n=120

traitA = (1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,8,8,8,8,8,8,8,8,9,9,9,9,9,9,9,10,10,10,10,10,10,11,11,11,11,11,12,12,12,12,13,13,13,14,14,15)
traitB = (2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,3,4,5,6,7,8,9,10,11,12,13,14,15,16,4,5,6,7,8,9,10,11,12,13,14,15,16,5,6,7,8,9,10,11,12,13,14,15,16,6,7,8,9,10,11,12,13,14,15,16,7,8,9,10,11,12,13,14,15,16,8,9,10,11,12,13,14,15,16,9,10,11,12,13,14,15,16,10,11,12,13,14,15,16,11,12,13,14,15,16,12,13,14,15,16,13,14,15,16,14,15,16,15,16,16)


for trait in $vars do
	munge_sumstats.py --sumstats {$trait}.txt --N 17115 --out $trait --merge-alleles w_hm3.snplist
done