This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How Can I Make An Ld Plot Of My Region Of Interest Using 1000 Genomes Data?

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 ld haplotype snp
• 11,437 views • link
updated by Biostar Biostar • written by mdgallagher71 • mdgallagher71

3 answers

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

• 1 views • link
written by JC JC

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.

• 0 views • link
written by mdgallagher71 • mdgallagher71

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)

• 0 views • link
written by ff.cc.cc ff.cc.cc

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

• 0 views • link
written by mdgallagher71 • mdgallagher71

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.

• 1 views • link
written by Maxime Lamontagne Maxime Lamontagne

Log in to answer this question.

More posts like this