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I have a long list of variant IDs that I generated as a result of research done one GRCh37 genomes (e.g. 13_28025615_G_C_b37). I want to get their rsIDs and compare them to a newly-obtained list of GRCh38 rsIDs that have also been retrieved from similarly formatted variant IDs (e.g. chr22_50473581_G_A_b38). How would I go about doing this? I've tried installing biomaRt as a package but I can't quite make heads or tails of it and it's not clear to me that it would support both versions of genome builds.

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it's not clear to me that it would support both versions of genome builds.

You can specify what version of the database you are querying.

I'd start with biomart on the ensembl website, see if you can get it to do what you want, then work on getting biomaRt to do what you want.

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  • $\begingroup$ ensembl.org/biomart/martview > CHOOSE DATASET > Ensembl Variation > I can't find any option for GRCh37, only 38 $\endgroup$ – CelineDion Sep 23 '19 at 19:20
  • $\begingroup$ The website might not have that enabled, but you can choose old versions in R. snpmart = useEnsembl(biomart = "snp", dataset="hsapiens_snp", version = 90) $\endgroup$ – swbarnes2 Sep 23 '19 at 19:37
  • $\begingroup$ When I do that, the only datasets I can see with listDatasets(snpmart) are GRCh38.p10. $\endgroup$ – CelineDion Sep 23 '19 at 19:47
  • $\begingroup$ Okay, I had to go all the way back to version 75 from Feb 2014 to get GRCh37. Thanks for your help. $\endgroup$ – CelineDion Sep 23 '19 at 19:50
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    $\begingroup$ Don't use the e75 version of BioMart, it's really out of date. There's a dedicated GRCh37 version where the variation database has been updated. More info here: ensembl.org/info/data/biomart/biomart_r_package.html $\endgroup$ – Emily_Ensembl Sep 24 '19 at 9:47

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