SNP (rsID) to chromsome:postion:REF:ALT

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23 months ago

MAPK2 ▴ 40

Hi All,

I was trying to find a tool within the UCSC web to convert SNP (rsIDs) to chromsome:postion:REF:ALT based on GRCh38. I just have about one hundred rsIDs to convert and don't want to loop over all annotated VCFs. Could someone please share the link if there are any available? Thanks!

dbsnp • 647 views

ADD COMMENT • link updated 23 months ago by Ram 43k • written 23 months ago by MAPK2 ▴ 40

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Search the forum, I'm sure this question has been addressed already.

ADD REPLY • link 23 months ago by Ram 43k

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I did, but couldn't find it. There was a mysql option for reverse conversion which does not work anymore.

ADD REPLY • link 23 months ago by MAPK2 ▴ 40

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You could always use either dbSNP API (if one is available) or download the appropriate dbSNP VCF file and query against it.

To find the appropriate dbSNP version, look into your VCF or your annotation pipeline - there should be a mention of the dbSNP version somewhere in there.

ADD REPLY • link 23 months ago by Ram 43k

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