Download whole 1000 genome phase 3 for LD clumping

Question

[ahmed.abdo]

Dear all,

I need to download the whole 1000 genome phase 3 for European to perform LD clumping using Plink.

Where I can download it? and there will be separated by chromosomes? and then I should merge them?

I tried globus.org, but I could not find those related to variants.

Any idea how to download it please?

Thanks in advance

Answer 1

[Vivek]

There's a few options to download the phase 3 VCFs here, including the NCBI FTP site: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp

[ahmed.abdo]

Thanks so much, but how download it, I click on the link and nothing appear.

[GenoMax]

Most browsers have turned ftp protocol access off so you can no longer use FTP links.

You can instead use https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/ to get to the link posted by @Vivek.

[ahmed.abdo]

Thanks, I did that