This may be a very simple question for you, but I am quite new to this so would like to ask for your help…
I am trying to understand the LD between SNPs found in the catalogue of published GWAS studies (http://www.genome.gov/gwastudies/) for a certain disease, and wanted to look at whole chromosomes at a time to understand the total genomic length that would need to be resequenced using NGS. I am trying to use LocuZoom (https://statgen.sph.umich.edu/locuszoom/genform.php?type=yourdata), but I need to specify a specific region on the chromosome and cannot plot a large area such as a chromosome. (For example I have 20 SNPs from different GWAS on chromosome 1, with genomic position ranging from 11852516 to 240445596.)
Would you have any suggestions regarding another software I could use to plot the LD between these SNPs on whole chromosomes, or what I could do to best split the chromosomes into regions to be plotted using LD?
I thank you very much for any help or suggestion. -f