<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>

CC BY-SA 4.0
2022-11-18T16:52:59.410Z
2022-11-18T16:52:59.410Z
Dandelion
<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>

CC BY-SA 4.0
2023-01-11T19:49:40.370Z
2023-01-11T19:49:40.370Z
Giulio Genovese
<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>

CC BY-SA 4.0
2022-11-18T10:46:54.930Z
Have you tried some tool or approach already?
JRodrigoF
CC BY-SA 4.0
2022-11-18T12:12:46.447Z
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.
terdon
<gwas><identifiers><liftover>
Lifting snp rsid build 37 to 38
# 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.  

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## 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.


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### 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


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