How to Select A Given Subset of SNPs from the 1000GP Dataset?

Question

[chiaoyu]

Dear Biostar Experts,

I am currently working on some SNPs dataset where I need to use the individual data for LD pruning. Since the original dataset doesn't come with individual data, I was told to use 1000GP's individual data to do the pruning. However, the dataset we are interested in contains around 2 millions SNPs, which is far less than that in 1000GP, so we need to find the SNPs in the intersection of these 2 million SNPs and those in the 1000GP. I wonder if there's a way to download only this intersection's data from 1000GP, or if that's not viable and we need to download the whole 1000GP, how we can select the subset in our machine.

Thanks a lot for any help!

Best, Chiao-Yu

Answer 1

[chrchang523]

The entire 1000GP phase 3 dataset is only a ~3.6 GiB download from https://www.cog-genomics.org/plink/2.0/resources , or ~3 GiB if you don't need the VCF annotations. From there, it should not be too difficult to intersect with your dataset.