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I want to do LD local clumping. The tutorial (https://mrcieu.github.io/ieugwasr/articles/local_ld.html) teaches how to, but the downloaded bfile is GRch37. I followed this question to download GRch38. LD clump GRCh38 GWAS results

I downloaded and it is "all_hg38.pgen". How can I transform it into bfile? Thank you.

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I have the same problem when facing the analysis of eQTL data for clumping and I do not find any answer to solve it. So I try to find a method to transform 1000 Genomes phase 3 ailgned by hg38 data which is pfile format (pgen, pvar, psam). I found a method at: https://cran.r-project.org/web/packages/snpsettest/vignettes/reference_1000Genomes.html. This is a method about how to extract the EUR population and transfrom to bfile format using PLINK 2.0. After this transfrom we can use PLINK 1.9 to clump the GWAS data. I think this is the method which we want to use and I will try it. Hope this can help you.

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