I have GWAS data. I have my data in 22 chromosome files in plink format. I have imputed genotype with Sanger imputation server. I use plink for my analysis but because plink 1.9 no more supports --hap https://www.cog-genomics.org/plink/1.9/ld and I'm facing issues with Beagle. I don't know how beagle works. and I have imputed and phased data. I would appreciate If I could get some help. I want to do linkage and haplotype analysis of GWAS data which has been phased and imputed.
I appreciate any help