Updating kgp IDs to RS id

[Fatemifar, Ghazaleh]

Hi,

 

I am trying to update my kgp IDs to rs IDs for SNPs typed on the illumina HumanOmni2.5M array.

I am aware that this can be carried out by creating a file with my genomic coordinates and then using the UCSC table browser to update the IDs. However, this method only allows you to update 1000 markers at any given time. I was wondering whether there is an alternative way of doing this, as would like to update all the kgp markers in our sample to rs IDs.

 

Many Thanks

 

Ghazaleh

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Dr Ghazaleh Fatemifar

Farr Institute of Health Informatics Research

Department of Epidemiology & Public Health

University College London

222 Euston Road

London

NW1 2DA

Tel: 0203 5495588

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[Matthew Speir]

Hi Ghazaleh,

Thank you for your question about converting your kgp IDs to rsIDs. Unfortunately, there doesn't seem to be an easy way to convert these, though we've had a few users ask us for advice on how to do so. Please see the answers to those previous mailing list questions for advice on how to convert these:

    https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/pdHJeMaXayw/SRwydWMnm_AJ
    https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/Rx4v-f5QVYI/CsOFlXSgwEkJ

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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