I'll greatly appreciate your help/advice regarding merging two sets of data with PLINK. I have a set of SNP genotypes in PLINK format and another one for biallelic deletions (recoded as 0 and 1) also in PLINK format. I want to generate a single file that gather all the genotypes for LD analysis of these deletions with neighbouring SNPs. I used the merge function of PLINK but was unable to get results for LD analysis. Is there anyone that can help me to handle such data ?