
# LD Score regression script to calculate genetic correlations
# From: https://github.com/bulik/ldsc


### MUNGE ###

# munge
./munge_sumstats.py \
--sumstats ./Revision/sumstats/SavageJansen_2018_intelligence_metaanalysis.txt \
--N 269867 \
--out intelligence \  # replace for other traits
--merge-alleles w_hm3.snplist


### LOOP FOR MULTIMORBIDITY GENETIC CORRELATIONS WITH RISK FACTORS ###

for trait in NikMahUKBB CAD-nikpay T2D-maha MD_UKBB
do
	for risk_factor in HDL LDL TG TC CRP insulin DBP SBP BMI body_fat current_smoking income maltreatment worry SESA insomnia neuroticism intelligence CAD-nikpay T2D-maha MD_UKBB
	do
		echo $trait $risk_factor
		./ldsc.py \
		--rg ${trait}.sumstats.gz,${risk_factor}.sumstats.gz \
		--ref-ld-chr eur_w_ld_chr/ \
		--w-ld-chr eur_w_ld_chr/ \
		--out ${trait}_${risk_factor}
	
	echo "********* Correlations between" $trait "and" $risk_factor "*********" >> multimorbidity_${risk_factor}_rg.log
	echo >> ./Revision/multimorbidity_${risk_factor}_rg.log
	sed '54,58!d' ${trait}_${risk_factor}_revision.log >> multimorbidity_${risk_factor}_rg.log

	done
done
