Linkage disequilibrium plots

Question

[tom.d.brocklehurst]

To complete post-QC analysis, I wanted to obtain an LD plot. After certain cut-off's I was left with a handful of SNP's and two were found on the same gene therefore I am thinking to expand on this region. What do I need to complete this? And will I need to state D' or r2 values?

Thanks, Tom

Answer 1

[vlaufer]

Well what statistics you include may depend on what exactly you are trying to show in this post-QC analysis.. but at any rate you might try

https://www.broadinstitute.org/mpg/snap/

or

http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/tutorial

Hope that helps, if not let us know more specifically what you are trying to show.

Good luck!