Hello, everyone,
I have difficulties dealing with the genotype file. I wonder if anyone can tell me how to convert file like "AMP-AD_ROSMAP_Rush-Broad_AffymetrixGenechip6_Imputed_chr12.dosage.gz" to plink format file? I have look for the answer in the previous forum but find nothing. Is any one can help me or give some tips? Thanks~
Yu
Created by Jintai Yu Yujintai Sorry for the late reply, I will try it. Thank you very much! As I said, plink has a mechanism to read in these files, so you can use it for GWAS. Thank you for your kind help here. As you have said, however, I want to use these "AMP-AD_ROSMAP_Rush-Broad_AffymetrixGenechip6_Imputed_chr12.dosage.gz" to do GWAS, do you have any good way to do GWAS using these data? Dosages are not well suited to plink format because they are expected values, not genotypes. You can read the data into plink, however: https://www.cog-genomics.org/plink/1.9/assoc#dosage.
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