UCSC Genome Browser Public Support- Convert Build 38 to Build 37

[Livia Soledade de Moraes Rego]

      I am finding, as a newbie in bioinformatic tools, the UCSC Genome Browser Public Support Group at Google a very useful forum.

     In one of these conversations (https://groups.google.com/a/soe.ucsc.edu/g/genome/c/M0UGFMJadrY), it was raised that it is not recommended to use LiftOver as a tool to lift SNPs. I am currently running genetic correlation between some summary statistics from GWAS using LDSC. One of them is in Build GRCh38, so I need to convert that to Build GRCh37. Is it possible to use the LiftOver in this case?

 Thanks very much,

       

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Livia S. M. Rego, MSc

PhD Student, PhysioGen Lab

Physiological Genomics of Mental Health,  

Institute of Biomedical Sciences, University of São Paulo, Brazil

(+55) 11 97485-9671

livia...@icb.usp.br| livia...@gmail.com

[Gerardo Perez]

Hello,

Thank you for your interest in the Genome Browser and for using the UCSC Genome Browser Public Support Group forum.

When lifting SNPs between human, it is highly recommended to use rsIDs and look up the updated coordinates in the target assembly's dbSNP table. You can use the list of rsIDs to query the updated coordinates from the source data. Looking both of these up this way in hg19 or hg38 result in the correct coordinates.

You can take a look at the following archived questions for details on how to accomplish this using the Table Browser: https://groups.google.com/a/soe.ucsc.edu/g/genome/c/SM0Ae7NMf4k/m/oh4_M8DeAgAJ

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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