Affy 500K positions in hg38
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5.6 years ago
Richard ▴ 580

Hi all,

Does anyone know where one can find a list of the Affy 500K SNP positions in hg38 coordinates?

affymetrix hg38 • 1.6k views
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5.6 years ago
Richard ▴ 580

If anyone needs to know how I ended up figuring this out.

I downloaded the annotation CSV files from here (these files have hg19 coords), and joined the rs IDs against a dbSNP VCF:

http://www.affymetrix.com/catalog/131459/AFFY/Mapping+500K+Array+Set#1_3

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5.6 years ago

As one of several solutions, I suspect, the UCSC genome browser has these data in a table snpArrayAffy6 but for hg19/GRCh37. Grab the data in bed format from the table browser and then use the UCSC liftover tool to move to hg38.

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Has anybody produced a bed file for the 23andme/Illumina/Affy rsIDs on hg38?

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