<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>

CC BY-SA 4.0
2024-01-25T09:05:31.377Z
2024-01-25T09:06:56.663Z
2024-01-25T09:06:56.663Z
Shuangpiji
<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>

<r><ld>
LD local clump-GRCh38 bfile
# 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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