Question: Making a standardized list of conversion of all kgp identifiers to RSids for the NHGRI GWAS catalog
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gravatar for Vincent Laufer
2.8 years ago by
Vincent Laufer1.0k
United States
Vincent Laufer1.0k wrote:

If you have ever bought an illumina DNA microarray, you are no doubt aware that they provide a lot of ids as "kgp" numbers instead of RSids (as well as other sorts of IDs). They also provide kgp-rs conversions in flat files that are available on their website or by request.

However, I have not bought any single Illumina chip, rather, I am analyzing the information in the NHGRI GWAS catalog, which presumably contains kgp ids from many different illumina chips.

In this catalog, the SNPs that have kgp ids not only do not have rsid equivalents, but also they do not have chr and pos provided either (example: https://www.ebi.ac.uk/gwas/search?query=kgp10769919#association ). As a result, I am having difficulty intersecting these with other resources.

As a result, my next step is to write to Illumina and try to obtain every kgp-rs flatfile they have ever made, then I will make one standardized resource, hopefully with not too much QC.

My question is, before doing this, is anyone aware if such a resource already exists (to reiterate, I'm after one file containing all these conversions, rather than for just one chip)?

snp rsid conversion kgp • 1.1k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Vincent Laufer1.0k

Hello. This would be amazing. Were you ever able to create this file or get the files from Illumina? Thank you!

Lisa

ADD REPLYlink written 2.6 years ago by lattarulol0
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