Question: Affy 500K positions in hg38
1
gravatar for Richard
3.8 years ago by
Richard570
Canada
Richard570 wrote:

Hi all,

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

affymetrix hg38 • 1.2k views
ADD COMMENTlink modified 3.8 years ago by Sean Davis25k • written 3.8 years ago by Richard570
1
gravatar for Richard
3.8 years ago by
Richard570
Canada
Richard570 wrote:

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

 

ADD COMMENTlink written 3.8 years ago by Richard570
0
gravatar for Sean Davis
3.8 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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.  

 

ADD COMMENTlink written 3.8 years ago by Sean Davis25k

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

ADD REPLYlink written 22 months ago by 141341254653464453.5k
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