How to Perform LD Pruning if I don't Have Individual Data?

Question

[chiaoyu]

Hi everyone,

I am a statistics PhD who tries to use some biology dataset to test the performance of our new multiple testing procedure. We got a dataset with about 2m SNPs (with marker RS id) and the corresponding Z-scores for several phenotypes. The original dataset may contain SNPs in linkage disequilibrium so we want to do some LD pruning based on the PLINK package (as was done in the previous literature). However, the dataset doesn't come with individual package, and I am not sure what to do with that. I am almost an outsider to biology and know very little about LD pruning...

Basically we have the map file that contains the SNP information, but miss the ped file that should contain the individual data. Is it still possible to do the pruning, and if so, how? Thank you very much for any help. I highly appreciate any suggestions!

Best, Chiao-Yu

Answer 1

[zx8754]

Yes, it is possible, we can download public genotype data, for example 1000 genomes project, extract overlapping SNPs with our data and matching population.

Then do pruning as usual, search for "plink LD pruning".