Re: [genome] LiftOver for SNP array

[Luvina Guruvadoo]

Hello Sandeep,

Thank you for your question. The liftOver tool will convert your coordinates from one assembly to another. In order to do this, your data should be in BED format, see the following page for more information: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert. We do not have a utility to convert PLINK to BED or vice versa. You might perform a web search to find such a utility. Otherwise, you would need to write a script to perform the conversion yourself.

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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

On Tue, Jul 14, 2015 at 9:53 AM, Sandeep Singhal <sksin...@gmail.com> wrote:

Hello,

I am trying to convert all my SNP data from different platform (mainly Affy and Illumina) to one built (i.e. Built 37 or Built 38). For SNP array BED file format is different that we received from Plink as compare to what has been provided on UCSC website (http://genome.ucsc.edu/FAQ/FAQformat.html#format1). Please let me know what would be the best way to perform this analysis using liftOver.

Thanks

Sandeep 

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