Hapmap phase3 in hg19 plink format

[Tuna, Salih]

Hi,

I would like to liftover Hapmap phase3 data in plink format to the hg19(b37). I only found this data to be available in b36. Is there a way to liftover plink format data which will also update the rs numbers for hg19?

Alternatively, is it available to download this from database if it is already been liftover in plink format?


Best,
Salih

[Steve Heitner]

Hello, Salih.

I assume you obtained the data directly from the International HapMap
Project at http://hapmap.ncbi.nlm.nih.gov/downloads/index.html.en. Our
liftOver utility is not compatible with PLINK format. To use the liftOver
utility, data should be in BED format (please refer to
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert).

We do have HapMap data already in BED format
(http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=hapmapSnps), but our
data is from Release 27 while the data available directly from the
International HapMap Project is Release 28. If you decide you would like to
download our data, it is available at
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/.

For the data in PLINK format, 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.

Also note that the liftOver utility will merely convert the genomic
coordinates from hg18 to hg19. It will not update rs numbers or perform any
other change on the underlying data.

Please contact us again at gen...@soe.ucsc.edu if you have any further
questions. 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.

---
Steve Heitner
UCSC Genome Bioinformatics Group

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