How Can I Make An Ld Plot Of My Region Of Interest Using 1000 Genomes Data?

Question

[mdgallagher71]

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

Answer 1

[JC]

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

[mdgallagher71]

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.

Answer 2

[ff.cc.cc]

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)

[mdgallagher71]

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

Answer 3

[Maxime Lamontagne]

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.