Answers.Body: <p>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: <a href="https://cran.r-project.org/web/packages/snpsettest/vignettes/reference_1000Genomes.html" rel="nofollow noreferrer">https://cran.r-project.org/web/packages/snpsettest/vignettes/reference_1000Genomes.html</a>. 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.</p>
  
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Answers.CreationDate: 2024-01-25T09:05:31.377Z
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Body: <p>I want to do LD local clumping.
  The tutorial (<a href="https://mrcieu.github.io/ieugwasr/articles/local_ld.html" rel="nofollow noreferrer">https://mrcieu.github.io/ieugwasr/articles/local_ld.html</a>) teaches how to, but the downloaded bfile is GRch37.
  I followed this question to download GRch38.
  <a href="https://bioinformatics.stackexchange.com/questions/21247/ld-clump-grch38-gwas-results">LD clump GRCh38 GWAS results</a></p>
  <p>I downloaded and it is &quot;all_hg38.pgen&quot;. How can I transform it into bfile? Thank you.</p>
  
Tags: <r><ld>
Title: LD local clump-GRCh38 bfile
ThreadText: # LD local clump-GRCh38 bfile
  
  (Asked by: username_0 on 2024-01-05)
  
  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](https://bioinformatics.stackexchange.com/questions/21247/ld-clump-grch38-gwas-results)
  
  I downloaded and it is "all\_hg38.pgen". How can I transform it into bfile? Thank you.
  
  **Tags:** r, ld
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2024-01-25. Score: 1
  
  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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