Question: Visualise Ld Plots On Whole Chromosome
1
gravatar for User 7754
8.0 years ago by
User 7754230
United Kingdom
User 7754230 wrote:

Dear all,

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

ADD COMMENTlink modified 8.0 years ago by Hitchpy0 • written 8.0 years ago by User 7754230
2
gravatar for Pierre Lindenbaum
8.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

Did you try haploview ? : http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview ( http://bioinformatics.oxfordjournals.org/content/21/2/263.full )

alt text

ADD COMMENTlink written 8.0 years ago by Pierre Lindenbaum121k
1

Sorry if I misunderstand you... But you should definitely use the genotypes from hapmap. All your SNPs should be there since you are interested in GWAS hits. You can download all Hapmap snps directly from haploview

ADD REPLYlink written 8.0 years ago by Thomas720

Hi and thank you for your reply. I have looked at Haploview but I had the impression I needed genotype information and could add a list of SNPs as 'tag SNPs' only after loading individual genotype data or association data from Plink, which I do not have…But maybe I am missing something, I'll look it up again...

ADD REPLYlink written 8.0 years ago by User 7754230

Thank you both for your answers. Thomas, I am stll trying to figure this out, since downloading just chromosome 1 in the HapMap Project data dumps format to then load it in the "Hapmap format" in Haploview takes too long (or does not work...it has been going for an hour...) Also, if I manage to download the data from HapMap and load it into Haploview, do I have to then individually go through each SNP to choose the ones that corresponds to the list I have? Thanks again

ADD REPLYlink written 8.0 years ago by User 7754230

I am a little confused why you want to look at the entire chromosome. I thought your purpose was to sequence regions around a gwas hit. (like a fine-mapping to locate putative functional snps)... and thus you wanted an idea of the LD structure around the gwas hit. For that purpose I would simply look up all SNPs as well as the 250kb regions surrounding the SNP (not the entire chr). Beyond 250kb you will find almost no LD with your hit.

ADD REPLYlink written 8.0 years ago by Thomas720

Hi Thomas, the purpose is actually to find out how long is the sequence to be resequenced using NGS, so I was trying to find out the length of haplotype blocks around the highly associated SNPs, and was wondering whether there was a quicker way to do this instead of looking at each single SNP (by visualising a whole chromosome for example). I found this software which could maybe help, although it is from 2006… http://bioinformatics.oxfordjournals.org/content/22/16/1933.full Do you know about it maybe? Thank you for all the help..

ADD REPLYlink written 8.0 years ago by User 7754230

No... sorry, But good luck

ADD REPLYlink written 8.0 years ago by Thomas720
0
gravatar for Hitchpy
8.0 years ago by
Hitchpy0
GZ China
Hitchpy0 wrote:

i don't know……but saw some people gave this answer in an earlier reply http://biostar.stackexchange.com/questions/10226/plot-ld-in-r-as-in-haploview

ADD COMMENTlink written 8.0 years ago by Hitchpy0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1685 users visited in the last hour