Repeated records in OpenTargets Genetics PheWAS table report?

Technical Support
1

In the Phewas table for this variant: Open Targets Genetics

I note that there are some study-associations that are repeated. A CSV export of one example pasted below - 5 records report the same association for the query variant.

Is that expected? Exploration of the source data files at ftp://ftp.ebi.ac.uk:21/pub/databases/opentargets/genetics/22.02.01/sa/gwas
seems to suggest to me that the repeated records are present in those source parquet files as well. Thanks for any insight.

otg_1_7689747_A_G
otg_1_7689747_A_G1560×213 28.9 KB

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2

Hi @hillan ,

Thank you for reporting this issue to us. We are investigating the causes. We’ll let you know about the details, or you can follow the progression on our issue tracker.

Best,
Daniel

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3

Hi @hillan,

After thoroughly investigating the problem, I could identify a number of issues that lead to duplication in our unfiltered GWAS dataset. Unfortunately, to resolve all of them, requires significant changes in a number of places of our pipelines, which will take a while. So at this point, I cannot give you a definite timeline, but you can expect a resolution close to the end of the year.

Thank you so much for reporting your finding, and please keep us notifying if anything else pops up! We highly value any feedback from our uses, although we might not be able to resolve all bugs quickly.

Best,
Daniel

4

Thanks @dsuveges - appreciate the work you and team are doing to maintain and improve this great resource. Look forward to eventual resolution.

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