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Key Error when trying to run data.process_gwas_file() #3

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pensive-bubble opened this issue Jan 3, 2025 · 0 comments
Open

Key Error when trying to run data.process_gwas_file() #3

pensive-bubble opened this issue Jan 3, 2025 · 0 comments

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@pensive-bubble
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pensive-bubble commented Jan 3, 2025

Hello,
I'm trying to run using my own GWAS summary statistics. My input file is below
Image 03-01-2025 at 10 58

When I reach data.process_gwas_file(), I get KeyError: 'rs62513865'. Do you know why this might be?
Image 03-01-2025 at 10 58

I have also tried to use another input file with just CHR, SNP, P, and N, but run into KeyError: 'BETA' when i run data.process_gwas_file(). Your documentation says I only require these 4 columns. Do you know what the issue is for this?

Finally, I don't seem to have an alternate allele frequency in my summary stats (https://pgc.unc.edu/for-researchers/download-results/ - I'm looking at the latest ED results). Will this be a problem?

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