Resolving Missing rsIDs in TOPMed Imputation Data for GWAS Analysis
I am using TOPMed imputation genotyping data for my GWAS analysis. However, during the QC steps, the output file contains many missing entries represented by dots ("."
) instead of rsIDs. Upon investigation, I realized that the .bgen
file does not include rsIDs. How can I resolve this issue?
Comments
1 comment
I got the same problem. My output file contains all entries as dots.
Sahar Mikaeeli , how do you investigate .bgen files? Can you share some snap of your codes?
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