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Hello! I have a new issue :)
When I try to add a GWAS track, using the 1.0.5 version, a Not Found error is raised:
If I check the tracks folder, there is no new file for the GWAS track. The pr…
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### System information
_No response_
### Description of the Issue
Hello, I installed gwas-sumstats-tools in a conda environment. But I get the following error message when I run gwas_ssf.
(gwas-su…
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We want to create a version of the staging data that complies with the following rules for a gentropy pipeline run.
This is a data-patching exercise with the intention to produce a clean run of the…
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Creating a ticket to follow up on the GWAS function to be called in bioflow :) would the end of May be a realistic deadline?
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Can we use GWAS dataset without MAF given, i mean if we dont have MAF so with out filtering can we use that datasets for LAVA?
and should we use only significant SNPS or all the SNPs?
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Hi there!
Thank you for the practical package. I have a question regarding the coloc.abf function when running it between my eQTL and GWAS data, both derived from the same samples. Here’s the code …
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**Describe the bug**
All GCST studies (102,780) have been marked as invalid. This has consequences in all datasets downstream.
**Observed behaviour**
The drop is explained by the QC flags:
```
…
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**Empty yaml file types**
Found 785 yamls with empty file types - GCSTs listed in attached .txt file:
[yamls-with-empty-filetypes.txt](https://api.zenhub.com/attachedFiles/eyJfcmFpbHMiOnsibWVzc2FnZSI6…
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I suggest to add the QC flag(s) to study index after GWAS QC.
A bit unclear how it interferes with other steps in GWAS catalog processing tho.
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Hi,
I noticed that some studies consider a situation where two traits have been measured in two distinct datasets of unrelated individuals. However, I wanna use this method to do colocalization wit…