Mapping Illumina Snp Ids To Proper Rs Ids

Question

[TJSingh]

I am currently working with Illumina's Omni snp chips. When I initially got the raw data, Illumina indexed the majority of the 1000 genomes SNPs with a kgp id. Because I cannot find any list that mapped kgp to rs ids (I contacted Illumina about this), I was wondering if anyone has an idea of any reliable approach that maps these two ids. The file only provides genomic location and the major or minor alleles.

[Irsan]

Maybe you can map kgp numbers to rs-numbers by intersecting the two in genomic locations with Bedtools: Analyzing Genomic Features?

[sbasit.phd]

did you mapped kgp to rs IDs? I also face same problem. If you have solution then kindly guide me as well

[shangzhener]

Hi, I want to know if you solve this problem because I face the same problem. Thank you!

Answer 1

[Istvan Albert]

Illumina will certainly (or shall I say absolutely should) have that information.

There are ways to figure out what you need but each require nontrivial effort and care and plus some extra decision making that you should not need to do. Keep asking them for the information. It should be on the web page that lists the files and specification for you chip.

[jambqc]

This helped me. Since I was using the chip "Infinium Omni2.5-8 v1.4 " I found the information I needed searching in the following path on Illumina's website: Support» Array Support» BeadChip Kits» Infinium Omni2.5-8 Kit» Downloads» Infinium Omni2.5-8 v1.4 Support Files s» Infinium Omni2.5-8 v1.4 Loci Name to rsID Conversion File

Answer 2

[samsara]

BiForcetoolbox might do what you want