Convert SNP names from kpg to rs?

[Amal Harrati]

Dear Sir or Madam,

Thank you in advance for taking my question.  We have genotype data for SNPs genotyped on the Illumina HumanOmni2.5M array in PLINK format. A majority of SNPs have dbSNPs rs id's, but I have a handful of SNPs (12) that do not have the dbSNP rs id's and are labelled using kpg ids.

Is there a way to convert the SNP ids to be rs names?  (I have listed the SNP names below.)

kgp4560299
kgp1703572
kgp5696875
kgp7673403
kgp4043337
kgp9153906
kgp9614205
kgp910500
kgp12522368
kgp6975417
kgp5076136
kgp9495611


Thank you so very much for your time.

Sincereley,

Amal Harrati

Amal Harrati
PhD Candidate
Department of Demography
UC Berkeley

[Jonathan Casper]

Hello Amal,

Thank you for your question about converting kpg ID numbers into dbSNP rsID numbers. There are a couple of ways for you to do this. One is to convert the locations of your kpg items into a BED file and use that to filter our dbSNP track. More information about how to do that is available in the answer to this mailing list question: https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/0pM24K2BrYs/discussion. Alternatively, if it is easier, you can convert your variants into pgSNP format (http://genome.ucsc.edu/FAQ/FAQformat.html#format10) and pass them as input into the Variant Annotation Integrator (http://genome.ucsc.edu/cgi-bin/hgVai). The VAI tool has an option to automatically list any known dbSNP variants that match its input. More information about how to do this is available at https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/Rx4v-f5QVYI/discussion.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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