Resolving Missing rsIDs in TOPMed Imputation Data for GWAS Analysis

Sahar Mikaeeli

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? 

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    Manzur Farazi

    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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