Answers.Body: <p>There are multiple tools to use for this. Might I suggest the following reads: <a href="https://genviz.org/module-01-intro/0001/06/02/liftoverTools/" rel="nofollow noreferrer">Introduction to liftover tools</a>, where they also refer to this usefull post <a href="https://www.biostars.org/p/65558/" rel="nofollow noreferrer">BioStars post</a>. Maybe also consider reading this paper for a word of caution: <a href="https://academic.oup.com/bib/article/22/5/bbab069/6210068?login=true" rel="nofollow noreferrer">Paper</a>.</p>
  <p>Maybe you can also clarify you question more, if these links do not help you with what you need.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-11-18T16:52:59.410Z
Answers.LastActivityDate: 2022-11-18T16:52:59.410Z
Answers.UserDisplayName: Dandelion
Answers.Body: <p>I have recently worked on a couple of <a href="https://github.com/freeseek/score" rel="nofollow noreferrer">tools</a> to do exactly this. They are +munge to convert summary statistics into files following the <a href="https://github.com/MRCIEU/gwas-vcf-specification" rel="nofollow noreferrer">GWAS-VCF specification</a> and +liftover to convert a VCF from one genome build to another. This will automatically take care of REF⇆ALT switches by flipping the effect size and it will correctly handle indels, if there are any, in your summary statistics file</p>
  
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Answers.CreationDate: 2023-01-11T19:49:40.370Z
Answers.LastActivityDate: 2023-01-11T19:49:40.370Z
Answers.UserDisplayName: Giulio Genovese
Body: <p>I’m looking to lift over a dataset of GWAS summary stats from build 37 to 38, including converting rsid. Downstream it is to be used for co-localisation with another dataset of build 38.</p>
  <p>Would anyone be able to help with code for doing this please?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-18T10:46:54.930Z
Comments.Text: Have you tried some tool or approach already?
Comments.UserDisplayName: JRodrigoF
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-18T12:12:46.447Z
Comments.Text: Should we assume you are working on human data? Are the SNPs in coding regions only or do you also have intronic or, even worse, intergenic? Please [edit] your question and give us some context. Ideally also an example of your input.
Comments.UserDisplayName: terdon
Tags: <gwas><identifiers><liftover>
Title: Lifting snp rsid build 37 to 38
ThreadText: # Lifting snp rsid build 37 to 38
  
  (Asked by: username_0 on 2022-11-18)
  
  I’m looking to lift over a dataset of GWAS summary stats from build 37 to 38, including converting rsid. Downstream it is to be used for co-localisation with another dataset of build 38.
  
  Would anyone be able to help with code for doing this please?
  
  **Tags:** gwas, identifiers, liftover
  
  > **Comments:**
  > **username_1**: Have you tried some tool or approach already?  
  > **username_2**: Should we assume you are working on human data? Are the SNPs in coding regions only or do you also have intronic or, even worse, intergenic? Please [edit] your question and give us some context. Ideally also an example of your input.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2022-11-18. Score: 1
  
  There are multiple tools to use for this. Might I suggest the following reads: [Introduction to liftover tools](https://genviz.org/module-01-intro/0001/06/02/liftoverTools/), where they also refer to this usefull post [BioStars post](https://www.biostars.org/p/65558/). Maybe also consider reading this paper for a word of caution: [Paper](https://academic.oup.com/bib/article/22/5/bbab069/6210068?login=true).
  
  Maybe you can also clarify you question more, if these links do not help you with what you need.
  
  
  ---
  
  ### Answer by username_4 on 2023-01-11. Score: 0
  
  I have recently worked on a couple of [tools](https://github.com/freeseek/score) to do exactly this. They are +munge to convert summary statistics into files following the [GWAS-VCF specification](https://github.com/MRCIEU/gwas-vcf-specification) and +liftover to convert a VCF from one genome build to another. This will automatically take care of REF⇆ALT switches by flipping the effect size and it will correctly handle indels, if there are any, in your summary statistics file
  
  
  ---
  
  