Entering edit mode
3.4 years ago
curious
▴
820
I am trying to find out if some build 38 GWAS results are inflated due to polygenic signal
I am trying to run the equivalent of these two steps from the tutorial from ldsc
munge_sumstats.py \
--sumstats my_results.txt \
--N 17115 \
--out my_sum_stats
ldsc.py \
--h2 my_results.sumstats.gz \
--ref-ld-chr eur_w_ld_chr/ \
--w-ld-chr eur_w_ld_chr/ \
--out my_results
The eur_w_ld_chr LD scores they give as example are 1000 genomes build 37, but it looks like they merge with user input on rsids. Assuming I work with rsids can I use these example LD scores to compute LD score regression intercept for build 38 summary stats?