Question: How Can I Make An Ld Plot Of My Region Of Interest Using 1000 Genomes Data?
1
gravatar for mdgallagher71
6.8 years ago by
United States
mdgallagher7120 wrote:

Hi, I used HaploView to access the HapMap data for caucasians to construct an LD plot of my genomic region of interest. I'd like to do the same using 1000 Genomes data to compare the results, but I don't know which program to use or how to download the data for just my region of interest, and just for caucasians.

Thanks,

Mike

1000genomes haplotype ld snp • 8.5k views
ADD COMMENTlink modified 4.2 years ago by Biostar ♦♦ 20 • written 6.8 years ago by mdgallagher7120
1
gravatar for JC
6.8 years ago by
JC7.7k
Mexico
JC7.7k wrote:

You can use SNAP for that: http://www.broadinstitute.org/mpg/snap/

ADD COMMENTlink written 6.8 years ago by JC7.7k

Sorry I guess I didn't mean that kind of LD plot, I mean the one that shows pairwise SNP LD values in an inverted triangle, like in HaploView.

ADD REPLYlink written 6.8 years ago by mdgallagher7120
1
gravatar for ff.cc.cc
6.8 years ago by
ff.cc.cc1.3k
European Union
ff.cc.cc1.3k wrote:

You can do it offline with haploview, its default option is to download hapmap data, but here and here you find instructions on how to import and work on 1k genomes data.

p.s. Thanks to Laura (+1)

ADD COMMENTlink written 6.8 years ago by ff.cc.cc1.3k

Thanks, but where can I find the Sample Population mapping file URL? I want to include only caucasians.

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by mdgallagher7120
0
gravatar for Maxime Lamontagne
6.8 years ago by
Qu├ębec
Maxime Lamontagne2.1k wrote:

Follow this post to import 1000 data in PLINK format (http://www.1000genomes.org/faq/can-i-convert-vcf-files-plinkped-format) and use Haploview after.

ADD COMMENTlink written 6.8 years ago by Maxime Lamontagne2.1k
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