<p>This is a common issue. Instead of lifting over your genomes, it might be computationally and conceptually easier just to lift over the summary statistics to GRCh37. Alternatively (and preferably), this is <strong>done for you</strong> for every GWAS published in the GWAS catalog. Simply click on the &quot;harmonized&quot; folder after clicking on &quot;download&quot; and you can download whatever build aligns with your genotype data.</p>

CC BY-SA 4.0
2023-10-29T18:19:33.490Z
I am sticking with generating vcf in GRCH37. Thanks anyway.
Shafayet Rahat
CC BY-SA 4.0
2023-10-29T19:07:36.810Z
@ShafayetRahat You'll also need to ensure the scorefile is b37 too
BigMistake
CC BY-SA 4.0
2023-10-29T20:21:34.470Z
ok, thanks for the tips
Shafayet Rahat
CC BY-SA 4.0
2023-10-11T15:34:49.173Z
2023-10-11T15:34:49.173Z
BigMistake
<p>You might want to check out <a href="https://github.com/hakyimlab/summary-gwas-imputation" rel="nofollow noreferrer">this tool</a> which contains some software to <a href="https://genome.sph.umich.edu/wiki/LiftOver" rel="nofollow noreferrer">liftover</a> your coordinates from one build to another.</p>

CC BY-SA 4.0
2022-03-09T08:46:34.177Z
2022-03-09T08:46:34.177Z
user438383
<p>I am learning GWAS study and PRS for predicting disease. I was aligning my sequencing data with GRCH38 reference panel. However, in the PRS analysis step, I found that most of the summary statistics are developed in GRCH37. It was a bit inconvenient for me because I have to convert vcf/snp file into GRCH37 which may end up losing some snps. I was checking this database <a href="https://www.ebi.ac.uk/gwas/downloads/summary-statistics" rel="nofollow noreferrer">link</a>.
Is there any database of summary statistics in GRCH38?</p>

CC BY-SA 4.0
2023-09-15T16:11:39.463Z
It's a good question, could you please consider upvoting/accepting the answer by user438383. It's definitely useful IMO.
M__
<gwas><polygenic-risk-score>
Summary statistics version problem
# Summary statistics version problem

(Asked by: username_0 on 2022-03-09)

I am learning GWAS study and PRS for predicting disease. I was aligning my sequencing data with GRCH38 reference panel. However, in the PRS analysis step, I found that most of the summary statistics are developed in GRCH37. It was a bit inconvenient for me because I have to convert vcf/snp file into GRCH37 which may end up losing some snps. I was checking this database [link](https://www.ebi.ac.uk/gwas/downloads/summary-statistics).
Is there any database of summary statistics in GRCH38?

**Tags:** gwas, polygenic-risk-score
> **Comments:**
> **username_1**: It's a good question, could you please consider upvoting/accepting the answer by user438383. It's definitely useful IMO.  

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## 2 answers

### Answer by username_2 on 2023-10-11. Score: 3 | Accepted answer

This is a common issue. Instead of lifting over your genomes, it might be computationally and conceptually easier just to lift over the summary statistics to GRCh37. Alternatively (and preferably), this is **done for you** for every GWAS published in the GWAS catalog. Simply click on the "harmonized" folder after clicking on "download" and you can download whatever build aligns with your genotype data.

> **Comments:**
> **username_0**: I am sticking with generating vcf in GRCH37. Thanks anyway.  
> **username_2**: @ShafayetRahat You'll also need to ensure the scorefile is b37 too  
> **username_0**: ok, thanks for the tips  

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### Answer by username_3 on 2022-03-09. Score: 2

You might want to check out [this tool](https://github.com/hakyimlab/summary-gwas-imputation) which contains some software to [liftover](https://genome.sph.umich.edu/wiki/LiftOver) your coordinates from one build to another.


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