Hi all! I was looking into using the full summary statistics from the open targets genetics portal (looking in the “sa_gwas” folder within the data downloads), and I found that only variants with P < 0.005 were included. Is there a location that has the full, unfiltered summary statistics? thank you!
Dear Abhukku,
welcome to our community and thanks for your question!
We don’t make full summary statistics available to the community, but only to partners and collaborators.
For the GWAS Catalog studies, I would suggest to download the full and harmonised summary statistics from their public FTP. You can find a list of studies with summary statistics (with download link) on this page.
I hope this helps!
Best wishes,
Annalisa
Thanks so much, that’s very helpful! As a follow-up, are the analyses (e.g. coloc, fine-mapping) done on the data filtered by the .005 p-value, or on the full summary stats? Thanks again for all of the help!
You are welcome!
The analyses you mention have all been performed on full sumstats.
The filtered dataset is mainly generated to build the PheWas plot.
Let us know if you have any further questions on this.
Best,
Annalisa
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