How can I estimate the linkage disequilibrium from my imputed data set?

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How can I estimate the linkage disequilibrium from my imputed data set?

asked 2016-05-13 09:38:45 -0600

Hi everyone, I'm new to this software and to this forum, I would need to estimate the linkage disequilibrium using my data. I have around 3000 individuals with a list of SNP genotyped and imputed. I would like to create a LD plot from my population. I would like to do this on a small region of around 100kb. my file is in this format:

Subjects          SNP1      SNP2        SNP3     SNP4
A01               0.02       0          0.5      ...
A02               0.45       1          0.57     ...
A03               1.6        2          0.3      ...
....              ....       ...        ...      ...

Any suggestion?

Thanks

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answered 2016-05-16 09:32:47 -0600

Jami Bartole
201 ●3 ●3 http://www.goldenhelix.co...

Hi Mario,

I am happy to help with your GenomeBrowse questions.

The stand-alone version of GenomeBrowse is for visualization of data only, it does not have the functionality to estimate LD between markers.

Linkage Disequilibrium estimations are available in our SNP & Variant Suite (SVS) product. You can see an example of this analysis in our tutorial at the following link.

http://doc.goldenhelix.com/SVS/tutorials/ldhaplotypeanalysis/index.html

You can request access to SVS by filling out a request on our website at the following link.

http://goldenhelix.com/products/SNP_Variation/index.html

Let us know if you have any further questions.

Thanks, Jami...

Golden Helix Support

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How can I estimate the linkage disequilibrium from my imputed data set?

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