PLINK - analyzing summary stats

Question

[loy_loy]

Hi everyone,

I want to do some basic analysis with GWAS summary stats. There is no genotype data available, as I downloaded them from publication resources. Apparently, one can use PLINK for LD score calculation (e.g. with a haplotype reference). I struggle to find the right commands. PLINK always checks for .map + .ped files, which I cannot create only from summary stats. I already checked various online documentations but I find it very confusing.

How can I analyze summary stats with PLINK?

Thank you!

Lynn

[Fabio Marroni]

You definitely can use plink to compute LD (and not LD score). However, since LD is the non-random association of alleles at two different positions, in order to measure LD you need to have allele frequencies and haplotype frequencies. In plink, haplotype frequencies are inferred from genotype data. Thus, I am afraid you cannot compute LD without genotypic data in plink.