linkage disequilibrium and haplotype analysis of GWAS .
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 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
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