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I have a list of SNPs (index SNPs). As my tagging SNPs, I want to use SNP data from here. The data has the following column headers: Chromosome, Position, MarkerName, Effect_allele, Non_Effect_allele, Beta, SE, Pvalue.

My ultimate aim is to identify SNPs in the tagging set that are in LD with each of index SNPs. I need to calculate r2 between index SNPs and tagging SNPs within 1MB window and get a table of index vs tagging SNPs (r2>0.8).

How can I use PLINK to carry out this work? I'm new to PLINK and LD clumping

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You can't generate LD statistics for summary data from SNPs, as the LD calculation relies on the comparison of variants at the genotype level. Plink expects data to be in a genotype matrix with either each marker for each line (probably better in your case), or each individual for each line. Plink v1.9, in particular, will accept VCF-formatted input files, when populated with 'GT' information that describes the variants for each individual.

If you're okay with using the 1000 genome population for calculating LD, plink v1.9-compatible datasets should be accessible from here.

If not, you'll need to discuss your project with IGAP to see if you can have access to genotype-level data for LD testing. That's unlikely, because there are personal identification issues associated with non-summary data.

There's comprehensive documentation about the LD command(s) on the Plink 1.9 website here.

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  • $\begingroup$ Thanks for your explanation @gringer. I will now use a plink v1.9-compatible dataset from 1000 genome and then use plink --noweb --bfile 1000genomefile --clump SNPfile --clump-field P --clump-p1 1.0001 --clump-p2 1.0001 --clump-r2 0.8 --clump-kb 1000 --out resultfile. But I'm unsure if line-by-line listing of SNPs on SNPfile will work and what the correct format should be. Any suggestions? $\endgroup$
    – user27976
    Nov 22 '17 at 12:48
  • $\begingroup$ EDIT: --clump-p1 0.0001 --clump-p2 0.0001 $\endgroup$
    – user27976
    Nov 22 '17 at 14:14

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