Hi all,
I have tried to calculate the LD matrix for SuSiE coloc using ieugwasr, which use plink to calculate that using a reference panel for summary-level gwas data. But that did not work out well maybe because of the allele order (https://github.com/MRCIEU/TwoSampleMR/issues/420). I wonder if the same problem could happen with caviar? Is there a recommended solid method to calculate the LD matrix as require as input for caviar? Thanks!
Hi all, I have tried to calculate the LD matrix for SuSiE coloc using ieugwasr, which use plink to calculate that using a reference panel for summary-level gwas data. But that did not work out well maybe because of the allele order (https://github.com/MRCIEU/TwoSampleMR/issues/420). I wonder if the same problem could happen with caviar? Is there a recommended solid method to calculate the LD matrix as require as input for caviar? Thanks!