Inquiry Regarding Column Definitions in GWAS Summary Imputation Output File

[Huang Zhaoran]

Dear Community,

I hope this message finds you well.

I am currently utilizing the gwas_summary_imputation tool available at https://github.com/hakyimlab/summary-gwas-imputation/tree/master/src/gwas_summary_imputation.py for imputing GWAS summary data. The output file generated by this tool contains 13 columns, which are as follows:

variant_id
panel_variant_id
chromosome
position
effect_allele
non_effect_allele
frequency
zscore
variance
imputation_status
n
n_indep
most_extreme_z
While I have a general understanding of some of these columns, I am seeking clarification on the exact meaning and context of each column to ensure accurate interpretation of the results. Could you please provide an explanation or a reference document that outlines the purpose and content of each column?

Your assistance in this matter would be greatly appreciated, as it will enable me to better understand and utilize the imputed GWAS summary data for my research.

Thank you very much for your time and consideration.

Best regards