PLINK Clumping d-prime or r2?

Question

[Filago]

Hello, I want to work with the Fuma tool in order to analyze my gwas data.

This tool has an integrated clumping step (for highly significant loci), however I have some low threshold loci, which I also want to look at, so I have to pre-clump my data with plink. For this issue I already downloaded the 1000g phase 3 data.

Based on the PLINK documentation it seems as the clumping is based on dprime. However, for FUMA I would need a r-squared based clumping. Any suggestions?

Thanks for your help!

Andreas

Answer 1

[Lemire]

You're mistaken, it's based on r2. From https://www.cog-genomics.org/plink/1.9/postproc#clump :

Sites which are less than 250 kb away from an index variant and have r2 larger than 0.5 with it are assigned to that index variant's clump (unless they have been previously been assigned to another clump, and --clump-allow-overlap is not in effect). These two thresholds can be changed with --clump-kb and --clump-r2, respectively.