can you use LD scores from build 37 reference to get LD score intercept on build 38 summary stats?
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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?

ld regression score • 909 views
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