Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-29T18:19:33.490Z
Answers.Text: I am sticking with generating vcf in GRCH37. Thanks anyway.
Answers.UserDisplayName: Shafayet Rahat
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-29T19:07:36.810Z
Answers.Text: @ShafayetRahat You'll also need to ensure the scorefile is b37 too
Answers.UserDisplayName: BigMistake
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-29T20:21:34.470Z
Answers.Text: ok, thanks for the tips
Answers.UserDisplayName: Shafayet Rahat
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-11T15:34:49.173Z
Answers.LastActivityDate: 2023-10-11T15:34:49.173Z
Answers.UserDisplayName: BigMistake
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-09T08:46:34.177Z
Answers.LastActivityDate: 2022-03-09T08:46:34.177Z
Answers.UserDisplayName: user438383
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-15T16:11:39.463Z
Comments.Text: It's a good question, could you please consider upvoting/accepting the answer by user438383. It's definitely useful IMO.
Comments.UserDisplayName: M__
Tags: <gwas><polygenic-risk-score>
Title: Summary statistics version problem
ThreadText: # 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 username_3. It's definitely useful IMO.  
  
  ---
  
  ## 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**: @username_0 You'll also need to ensure the scorefile is b37 too  
  > **username_0**: ok, thanks for the tips  
  
  ---
  
  ### 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.
  
  
  ---
  
  