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I have an old set of pig SNP data and the positions were mapped using v10.2 of the assembly.

I submitted a GWAS paper for review, and the reviewer wants to know if any of the significant SNPs that were located in previously unknown genes are now in known genes, with the release of the latest assembly last year.

I was under the impression that I had to use the assembly the marker map was based on to see where SNPs are located. Is this correct or can I use the new assembly?

Many thanks in advance!

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Why haven't you tried using LiftOver to convert the coordinates?

https://genome.ucsc.edu/cgi-bin/hgLiftOver

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  • $\begingroup$ I didn't even know this was possible! Thank you! $\endgroup$
    – Trace
    Oct 11 '18 at 13:51
  • $\begingroup$ Hello! This question was deemed worth of an answer, so why not upvote it? Vote early, vote often to encourage new users and keep the community alive! $\endgroup$
    – LinuxBlanket
    Oct 11 '18 at 22:22

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