I have a question on eQTL nominal file input prep for CAVIAR. Lets, say If a SNP1 is in 1Mb window of a gene 1 and also in gene 2. Then how do we filter that out? because LD matrix is only for unique SNPs and CAVIAR needs zscore value for SNPs that are input in LD matrix.
I have a question on eQTL nominal file input prep for CAVIAR. Lets, say If a SNP1 is in 1Mb window of a gene 1 and also in gene 2. Then how do we filter that out? because LD matrix is only for unique SNPs and CAVIAR needs zscore value for SNPs that are input in LD matrix.