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Hi Louise,
I'm hoping you can help me. I've got a genetic exposure (SNP dosage) and a subset of UKB variables (1508) and am attempting to run PHESANT. I ran addNewFields.sh to update outcome-info.t…
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Hello,
My group has seen the PheWAS package use all available system resources and take a very long time to complete, even on smaller datasets. I'm fairly certain that this is happening because the…
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Dear Dr. Zhou,
I am wondering how to estimate the cost for each GWAS in AWS with UKBB (500K array data or 50K WES data). Did you have any estimation before since you already have UKB-SAIGE-PheWAS.…
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should the data we serve be somewhat filtered?
while we need the full data for finemapping and coloc, we may not need the non-significant data for regional plot + phewas?
it would help the database/…
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@emschmidt has created categories for the UKB phenotypes to be used in PheWAS. (opentargets/issues#2153)
Todo:
- [x] Merge field codes to our study table
- [x] Make LUT and upload to `gs://geneti…
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To be used in a future version of the PheWAS plot.
Biogen may have a pre-existing map for UK Biobank traits (as seen in a presentation of theirs). Alternatively it could be based on EFO codes, e.g.…
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I have added a new column (`trait_category` nullable string) to the study table. This will be used by Eliseo for the phewas api.
The modified table is in staging (`gs://genetics-portal-staging/v2d/…
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Currently the PheWAS plot on the variant page contains information on the variant in both UK Biobank and GWAS Catalog.
 for 2.2.4 and 3.0 version and notice there is a slight/very tiny difference on beta and P-value (at the 6th digit a…
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URL:
https://dev--genetics-app.netlify.app/variant/1_154453788_C_T
Variable:
```
{"variantId": "1_154453788_C_T"}
```
GQL API Query
```
query VariantPageQuery($variantId: String!) {
…