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!