Anyone Has A Hg18 Annotation File For Humanomni5-Quad?
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12.1 years ago
Rossella ▴ 370

Hi, I just got a HumanOmni5-Quad dataset and I realized that their manifest file is hg19 while the rest of my data is hg18. Does anyone have a hg18 annotation for this chip? The only thing I have been able to think of is to use the lift up option of ucsc but in that case I lose quite a lot of SNPs.

Any help/suggestion would be greatly appreciated! Thanks Rossella

illumina • 2.4k views
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12.1 years ago
ff.cc.cc ★ 1.3k

Did you have a look at the liftover tool from UCSC ? http://genome.ucsc.edu/cgi-bin/hgLiftOver

It is available online, and for linux workstations

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I took a look at it but it seems that some of the SNPs cannot be lift over. Do you have an idea why that would be? It is the first time I use it. Thanks

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You could systematically look (better with a script) for rsids of your Omniquad chip into a dbsnp release of NCBI36 (hg18) e.g. ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/b130_archive/b130_SNPChrPosOnRef_36_3.bcp.gz and then retrieve hg18 position. Have a look here too: http://genome.sph.umich.edu/wiki/LiftOver#Various_reasons_that_lift_over_can_fail

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Thanks a lot for your help

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