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? 

Comments

3 comments

Date Votes
  • Comment author
    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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  • Comment author
    Ilakya Selvarajan

    Hi! This problem still persists. Any solutions for resolving TOPMed imputed data QC?

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  • Comment author
    Maizy Brasher

    Hi! I am running into this problem also. Did anyone ever get a solution?
     

    This is a major barrier to transition to the RAP when using any software that refers to SNPs specifically by ID (ex. REGENIE --interaction-snp or --condition-list). I have seen suggestions elsewhere to use plink to set IDs, but it isn't reasonable to pay to store copies of these large genetic data files with the IDs filled in.

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