Question: Build 21 - Which Hg (Liftover)?
0
gravatar for zx8754
6.1 years ago by
zx87545.4k
London
zx87545.4k wrote:

Hope an easy one.

I have a genotyped data (Illumina Infinium HumanHap550) and was told it is Build 21. I need to LiftOver it to the latest build GRCh37/hg19. Found this website http://genome-archive.cse.ucsc.edu/downloads.html#human to get LiftOver "chain files". Can you tell me which hg corresponds to Build 21? Any advice on LiftOver would be useful, too.

Thanks

liftover • 1.5k views
ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 6.1 years ago by zx87545.4k
4
gravatar for Istvan Albert
6.1 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:

I think you were told an incorrect build number, See the link below for the naming conventions:

http://genome.ucsc.edu/FAQ/FAQreleases.html#release1

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Istvan Albert ♦♦ 77k
0
gravatar for Simon Cockell
6.1 years ago by
Simon Cockell7.3k
Newcastle
Simon Cockell7.3k wrote:

The only alternative I can think of is that the data is based on HapMap release 21...

ftp://ftp.ncbi.nlm.nih.gov/hapmap/00README.releasenotes_rel21

Which is itself based on hg17.

A quick Google suggests this is certainly plausible, for example, the UCSC track from the chip suggests that annotation is based on HapMap 20 (https://cgwb.nci.nih.gov/cgi-bin/hgTrackUi?g=snpArray).

ADD COMMENTlink written 6.1 years ago by Simon Cockell7.3k
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